1d7e

CRYSTAL STRUCTURE OF THE P65 CRYSTAL FORM OF PHOTOACTIVE YELLOW PROTEIN

Method: X-RAY DIFFRACTION D_max: 43.7 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

PHOTOACTIVE YELLOW PROTEIN

Halorhodospira halophila

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 4–125	Not recorded	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；290 K；PEG 2K, MES., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 17K	Resolution 1.39 Å R-free 0.198

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1D7E	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1F98 CRYSTAL STRUCTURE OF THE PHOTOACTIVE YELLOW PROTEIN MUTANT T50V Deposited 2000-07-07	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Mutation：T50V	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；292 K；Ammonium Sulfate, HEPES, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 292.0K	Resolution 1.15 Å R-free 0.176
1F9I CRYSTAL STRUCTURE OF THE PHOTOACTIVE YELLOW PROTEIN MUTANT Y42F Deposited 2000-07-10	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Mutation：Y42F	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；292 K；Ammonium Sulfate, HEPES, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 292.0K	Resolution 1.10 Å R-free 0.171
1GSV Crystal structure of the P65 crystal form of photoactive yellow protein G47S mutant Deposited 2002-01-08	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Mutation：YES	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；PEG 2K, MES., pH 6.50	Resolution 1.75 Å R-free 0.246
1GSW CRYSTAL STRUCTURE OF THE P65 CRYSTAL FORM OF PHOTOACTIVE YELLOW PROTEIN G51S MUTANT Deposited 2002-01-09	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Mutation：YES	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；PEG 2K, MES., pH 6.50	Resolution 1.85 Å R-free 0.230
1GSX CRYSTAL STRUCTURE OF THE P65 CRYSTAL FORM OF PHOTOACTIVE YELLOW PROTEIN G47S/G51S MUTANT Deposited 2002-01-09	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Mutation：YES	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；PEG 2K, MES., pH 6.50	Resolution 1.79 Å R-free 0.238
1KOU Crystal Structure of the Photoactive Yellow Protein Reconstituted with Caffeic Acid at 1.16 A Resolution Deposited 2001-12-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Not recorded	DHC CAFFEIC ACID × 1 NBU N-BUTANE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；290 K；PEGMME 2000, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 1.16 Å R-free 0.203
1NWZ PYP Ultra-high resolution structure of a Bacterial Photoreceptor Deposited 2003-02-07	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Not recorded	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；~2.5 M NH4SO4 20 mM Sodium Phosphate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 0.82 Å R-free 0.144
1ODV Photoactive yellow protein 1-25 deletion mutant Deposited 2003-03-14	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–125（100 aa） Fragment：RESIDUES 26-125	Not recorded	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；CRYSTALS WERE GROWN BY EQUILIBRATION OF 1 ML OF 30 MG/ML PROTEIN WITH 1 ML OF MOTHER LIQUOR (1.8 M AMMONIUM SULPHATE, 10 MM COCL[2], 100 MM MES PH 6.5) AGAINST A 1 ML RESERVOIR OF MOTHER LIQUOR. CRYSTALS APPEARED AFTER 2-3 DAYS A LARGEST DIMENSION OF 0.4 MM.	Resolution 1.14 Å R-free 0.177
1ODV Photoactive yellow protein 1-25 deletion mutant Deposited 2003-03-14	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 26–125（100 aa） Fragment：RESIDUES 26-125	Not recorded	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；CRYSTALS WERE GROWN BY EQUILIBRATION OF 1 ML OF 30 MG/ML PROTEIN WITH 1 ML OF MOTHER LIQUOR (1.8 M AMMONIUM SULPHATE, 10 MM COCL[2], 100 MM MES PH 6.5) AGAINST A 1 ML RESERVOIR OF MOTHER LIQUOR. CRYSTALS APPEARED AFTER 2-3 DAYS A LARGEST DIMENSION OF 0.4 MM.	Resolution 1.14 Å R-free 0.177
1OT6 CRYOTRAPPED CRYSTAL STRUCTURE OF THE E46Q MUTANT OF PHOTOACTIVE YELLOW PROTEIN UNDER CONTINUOUS ILLUMINATION AT 110K Deposited 2003-03-21	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Mutation：E46Q	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；ammonium sulphate, sodium phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 110K	Resolution 0.95 Å R-free 0.161
1OT9 CRYOTRAPPED STATE IN WILD TYPE PHOTOACTIVE YELLOW PROTEIN, INDUCED WITH CONTINUOUS ILLUMINATION AT 110K Deposited 2003-03-21	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Not recorded	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；ammonium sulphate, sodium phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 110K	Resolution 1.00 Å R-free 0.161
1OTA E46Q MUTANT OF PHOTOACTIVE YELLOW PROTEIN, P63 AT 295K Deposited 2003-03-21	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Mutation：E46Q	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；ammonium sulphate, sodium phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.10 Å R-free 0.180
1OTB WILD TYPE PHOTOACTIVE YELLOW PROTEIN, P63 AT 295K Deposited 2003-03-21	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Not recorded	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；ammonium sulphate, sodium phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.10 Å R-free 0.161
1OTD STRONG HYDROGEN BONDS IN PHOTOACTIVE YELLOW PROTEIN AND THEIR ROLE IN ITS PHOTOCYCLE Deposited 2003-03-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Not recorded	HC4 4'-HYDROXYCINNAMIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.5；PEG 4000, MgCl2, Tris, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 110K	Resolution 1.25 Å R-free 0.215
1OTD STRONG HYDROGEN BONDS IN PHOTOACTIVE YELLOW PROTEIN AND THEIR ROLE IN ITS PHOTOCYCLE Deposited 2003-03-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–125（125 aa）	Not recorded	HC4 4'-HYDROXYCINNAMIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.5；PEG 4000, MgCl2, Tris, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 110K	Resolution 1.25 Å R-free 0.215
1OTE E46Q MUTANT OF PHOTOACTIVE YELLOW PROTEIN, P65 AT 110K Deposited 2003-03-21	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Mutation：E46Q	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；PEG 2000, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 110K	Resolution 1.40 Å R-free 0.228
1OTI E46Q MUTANT OF PHOTOACTIVE YELLOW PROTEIN, P65 AT 295K Deposited 2003-03-21	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Mutation：E46Q	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；PEG 2000, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.40 Å R-free 0.161
1S1Y Photoactivated chromophore conformation in Photoactive Yellow Protein (E46Q mutant) from 10 microseconds to 3 milliseconds Deposited 2004-01-07	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Mutation：E46Q	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；ammonium sulfate, sodium phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.60 Å R-free 0.070
1S1Z Photoactivated chromophore conformation in Photoactive Yellow Protein (E46Q mutant) from 10 to 500 nanoseconds Deposited 2004-01-07	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Mutation：E46Q	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；ammonium sulfate, sodium phosphate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.60 Å R-free 0.060
1S4R Structure of a reaction intermediate in the photocycle of PYP extracted by a SVD-driven analysis Deposited 2004-01-17	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Not recorded	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；Ammoniumsulfate, potassium phosphate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.90 Å R-free 0.259
1S4S Reaction Intermediate in the Photocycle of PYP, intermediate occupied between 100 micro-seconds to 5 milli-seconds Deposited 2004-01-17	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Not recorded	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；Ammoniumsulphate, Potassium Phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.90 Å R-free 0.289
1T18 Early intermediate IE1 from time-resolved crystallography of the E46Q mutant of PYP Deposited 2004-04-15	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Mutation：E46Q	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；ammonium sulfate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.60 Å R-free 0.247
1T19 Early intermediate IE2 from time-resolved crystallography of the E46Q mutant of PYP Deposited 2004-04-15	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Mutation：E46Q mutant	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；ammonium sulfate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.60 Å R-free 0.219
1T1A Late intermediate IL1 from time-resolved crystallography of the E46Q mutant of PYP Deposited 2004-04-15	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Mutation：E46Q	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；ammonium sulfate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.60 Å R-free 0.331
1T1B Late intermediate IL2 from time-resolved crystallography of the E46Q mutant of PYP Deposited 2004-04-15	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Mutation：E46Q	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；ammonium sulfate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.60 Å R-free 0.332
1T1C Late intermediate IL3 from time-resolved crystallography of the E46Q mutant of PYP Deposited 2004-04-15	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Mutation：E46Q	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；ammonium sulfate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.60 Å R-free 0.139
1TS0 Structure of the pB1 intermediate from time-resolved Laue crystallography Deposited 2004-06-21	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Not recorded	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；2.6 M ammonium sulfate, 50 mM sodium phosphate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.60 Å R-free 0.116
1TS6 Structure of the pB2 intermediate from time-resolved Laue crystallography Deposited 2004-06-21	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Not recorded	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；2.6 M ammonium sulfate, 50 mM sodium phosphate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.60 Å R-free 0.186
1TS7 Structure of the pR cis wobble and pR E46Q intermediates from time-resolved Laue crystallography Deposited 2004-06-21	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Not recorded	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；2.6 M ammonium sulfate, 50 mM sodium phosphate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.60 Å R-free 0.391
1TS8 Structure of the pR cis planar intermediate from time-resolved Laue crystallography Deposited 2004-06-21	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Not recorded	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；2.6 M ammonium sulfate, 50 mM sodium phosphate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.60 Å R-free 0.383
1UGU Crystal structure of PYP E46Q mutant Deposited 2003-06-19	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Mutation：E46Q	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEGMME 2000, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.20 Å R-free 0.191
1UWN The Initial Events in the Photocycle of Photoactive Yellow Protein: A Common Mechanism on Light Activation in Photoreceptor Proteins Deposited 2004-02-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 1–125（125 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	HC4 4'-HYDROXYCINNAMIC ACID × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；2.25 M NH4SO4, 20 MM SODIUM PHOSPHATE PH 7, VAPOR DIFFUSION, HANGING DROP, TEMP 298K	Resolution 1.20 Å R-free 0.147
1UWP Initial Events in the Photocycle of Photoactive Yellow Protein Deposited 2004-02-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 1–125（125 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	HC4 4'-HYDROXYCINNAMIC ACID × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；2.25 M NH4SO4, 20 MM SODIUM PHOSPHATE PH 7, VAPOR DIFFUSION, HANGING DROP, TEMP 298K	Resolution 1.20 Å R-free 0.157
1XFN NMR structure of the ground state of the photoactive yellow protein lacking the N-terminal part Deposited 2004-09-15	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–125（100 aa） Fragment：residues 26-125	Not recorded	HC4 4'-HYDROXYCINNAMIC ACID × 1	SOLUTION NMR NMR measurement conditions pH 7；293 K；Ionic strength (raw mmCIF value) 50mM phosphate buffer；Pressure ambient NMR sample composition 1mM Delta25-PYP, 15N-13C, 50mM phosphate buffer \| 90% H2O/10% D2O NMR sample composition 1mM Delta25-PYP 15N, 50mM phosphate buffer \| 90% H2O/10% D2O	Resolution not provided
1XFQ structure of the blue shifted intermediate state of the photoactive yellow protein lacking the N-terminal part Deposited 2004-09-15	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–125（100 aa） Fragment：residues 26-125	Not recorded	HC4 4'-HYDROXYCINNAMIC ACID × 1	SOLUTION NMR NMR measurement conditions pH 7；293 K；Ionic strength (raw mmCIF value) 50mM phosphate buffer；Pressure ambient NMR sample composition 1mM Delta25-PYP, 15N-13C, 50mM phosphate buffer \| 90% H2O/10% D2O NMR sample composition 1mM Delta25-PYP 15N, 50mM phosphate buffer \| 90% H2O/10% D2O	Resolution not provided
2D01 Wild Type Photoactive Yellow Protein, P65 Form Deposited 2005-07-21	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Not recorded	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；40% PEG2000, 100mM sodium citrate, pH 6.5, VAPOR DIFFUSION, temperature 293K	Resolution 1.34 Å R-free 0.189
2D02 R52Q Mutant of Photoactive Yellow Protein, P65 Form Deposited 2005-07-21	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Mutation：R52Q	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；40% PEG2000, 100mM sodium citrate, pH 6.0, VAPOR DIFFUSION, temperature 293K	Resolution 1.42 Å R-free 0.163
2I9V Structural role of Y98 in PYP: effects on fluorescence, gateway and photocycle recovery Deposited 2006-09-06	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Mutation：Y98Q	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；293 K；3.2 M ammonium sulphate, 20 mM sodium phosphate, pH 5.9 , VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.241
2KX6 Signaling state of Photoactive Yellow Protein Deposited 2010-04-27	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Not recorded	HC4 4'-HYDROXYCINNAMIC ACID × 1	Experimental method not declared NMR measurement conditions pH 5.75；298 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR measurement conditions pH 7.5；50 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 50；Pressure ambient NMR sample composition 75 uM PYP, 50 mM potassium phosphate, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 75 uM PYP, 50 mM TRIS, 10 % glycerol, 50 mM Tris \| 50 mM Tris NMR sample composition 4.4 mM PYP, 50-200 mM Sodium phosphate, 20 mM sodium chloride, H2O \| H2O	Resolution not provided
2PHY PHOTOACTIVE YELLOW PROTEIN, DARK STATE (UNBLEACHED) Deposited 1995-04-12	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Not recorded	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.40 Å R-free 0.226
2PYP PHOTOACTIVE YELLOW PROTEIN, PHOTOSTATIONARY STATE, 50% GROUND STATE, 50% BLEACHED Deposited 1997-02-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.8；pH 4.8	Resolution 1.90 Å
2PYR PHOTOACTIVE YELLOW PROTEIN, 1 NANOSECOND INTERMEDIATE (287K) Deposited 1998-03-04	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Not recorded	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 1.90 Å
2QJ5 PYP ultra-high resolution of a bacterial photoreceptor Deposited 2007-07-06	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Not recorded	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；298 K；39% PEG 3000, 50 mM Tris-HCl pH 9, 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.20 Å R-free 0.219
2QJ7 PYP ultra-high resolution of a bacterial photoreceptor Deposited 2007-07-06	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Not recorded	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；298 K；39% PEG 3000, 50 mM Tris pH 9, 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.05 Å R-free 0.183
2QWS Neutron and X-ray structural studies of short hydrogen bonds in Photoactive Yellow Protein (PYP) Deposited 2007-08-10	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Not recorded	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；293 K；2.6 M ammonium sulfate in 50 mM sodium phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.00	Resolution 2.50 Å R-free 0.273
2ZOH X-ray Crystal Structure of Photoactive Yellow Protein, Wild type, at 295K Deposited 2008-05-20	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Not recorded	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP, MICROSEEDING；pH 9；295 K；AMMONIUM SULPHATE, SODIUM CHLORIDE, SODIUM DIDEUTERIUM PHOSPHATE, DISODIUM DEUTERIUM PHOSPHATE, pH 9.0, VAPOR DIFFUSION, HANGING DROP, MICROSEEDING, temperature 295K	Resolution 1.25 Å R-free 0.149
2ZOI Neutron Crystal Structure of Photoactive Yellow Protein, Wild type, at 295K Deposited 2008-05-21	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Not recorded	HC4 4'-HYDROXYCINNAMIC ACID × 1	NEUTRON DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP, MICROSEEDING；pH 9；295 K；AMMONIUM SULPHATE, SODIUM CHLORIDE, SODIUM DIDEUTERIUM PHOSPHATE, DISODIUM DEUTERIUM PHOSPHATE, pH 9.0, VAPOR DIFFUSION, HANGING DROP, MICROSEEDING, temperature 295K	Resolution 1.50 Å R-free 0.219
3PHY PHOTOACTIVE YELLOW PROTEIN, DARK STATE (UNBLEACHED), SOLUTION STRUCTURE, NMR, 26 STRUCTURES Deposited 1998-02-06	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Not recorded	HC4 4'-HYDROXYCINNAMIC ACID × 1	SOLUTION NMR NMR measurement conditions pH 5.8；311 K	Resolution not provided
3PYP PHOTOACTIVE YELLOW PROTEIN, CRYOTRAPPED EARLY LIGHT CYCLE INTERMEDIATE Deposited 1998-07-28	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Not recorded	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.8；pH 4.8	Resolution 0.85 Å R-free 0.155
3UMD Structure of pB intermediate of Photoactive yellow protein (PYP) at pH 4. Deposited 2011-11-13	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Not recorded	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；293 K；3 M Ammonium Sulfate, 50 mM Sodium Phosphate, pH 4, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.80 Å R-free 0.238
3UME Structure of pB intermediate of Photoactive yellow protein (PYP) at pH 7 Deposited 2011-11-13	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Not recorded	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；3.0 M Ammonium Sulfate, 50 mM Sodium Phosphate, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.80 Å R-free 0.146
3VE3 Structure of IT Intermediate from time-resolved laue crystallography Deposited 2012-01-07	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Not recorded	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；2.6M AMMONIUM SULFATE, 50MM SODIUM PHOSPHATE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.60 Å R-free 0.291
3VE4 Structures of ICT and PR1 intermediates from time-resolved laue crystallography Deposited 2012-01-07	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Not recorded	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；2.6M AMMONIUM SULFATE, 50MM SODIUM PHOSPHATE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.60 Å R-free 0.252
4B9O The PR0 Photocycle Intermediate of Photoactive Yellow Protein Deposited 2012-09-06	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Not recorded	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；295 K；2.2 M AMMONIUM SULFATE, 1.0 M SODIUM CHLORIDE, AND 10 MM SODIUM DIDEUTERIUM PHOSPHATE, 10 MM DISODIUM DEUTERIUM PHOSPHATE, PH 9.0, VAPOR DIFFUSION, HANGING DROP, MICROSEEDING, TEMPERATURE 295 K	Resolution 1.60 Å R-free 0.293
4BBT The PR1 Photocycle Intermediate of Photoactive Yellow Protein Deposited 2012-09-27	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Not recorded	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；295 K；2.2 M AMMONIUM SULFATE, 1.0 M SODIUM CHLORIDE, AND 10 MM SODIUM DIDEUTERIUM PHOSPHATE, 10 MM DISODIUM DEUTERIUM PHOSPHATE, PH 9.0, VAPOUR DIFFUSION, HANGING DROP, MICROSEEDING, TEMPERATURE 295 K	Resolution 1.60 Å R-free 0.228
4BBU The PR2 Photocycle Intermediate of Photoactive Yellow Protein Deposited 2012-09-27	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Not recorded	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；295 K；2.2 M AMMONIUM SULFATE, 1.0 M SODIUM CHLORIDE, AND 10 MM SODIUM DIDEUTERIUM PHOSPHATE, 10 MM DISODIUM DEUTERIUM PHOSPHATE, PH 9.0, VAPOUR DIFFUSION, HANGING DROP, MICROSEEDING, TEMPERATURE 295 K	Resolution 1.60 Å R-free 0.218
4BBV The PB0 Photocycle Intermediate of Photoactive Yellow Protein Deposited 2012-09-28	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Not recorded	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；295 K；2.2 M AMMONIUM SULFATE, 1.0 M SODIUM CHLORIDE, AND 10 MM SODIUM DIDEUTERIUM PHOSPHATE, 10 MM DISODIUM DEUTERIUM PHOSPHATE, PH 9.0, VAPOUR DIFFUSION, HANGING DROP, MICROSEEDING, TEMPERATURE 295 K	Resolution 1.60 Å R-free 0.360
4HY8 Structures of PR1 and PR2 intermediates from time-resolved laue crystallography Deposited 2012-11-13	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Not recorded	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；2.6M AMMONIUM SULFATE, 50MM SODIUM PHOSPHATE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.60 Å R-free 0.275
4I38 Structures of IT intermediates from time-resolved laue crystallography collected at 14ID-B, APS Deposited 2012-11-26	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Not recorded	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop；pH 7；298 K；2.6M AMMONIUM SULFATE, 50MM SODIUM PHOSPHATE, pH 7.0, hanging drop, temperature 298K	Resolution 1.60 Å R-free 0.285
4I39 Structures of ICT and PR1 intermediates from time-resolved laue crystallography collected at 14ID-B, APS Deposited 2012-11-26	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Not recorded	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；2.6M AMMONIUM SULFATE, 50MM SODIUM PHOSPHATE, pH 7.0, temperature 298K, VAPOR DIFFUSION, HANGING DROP	Resolution 1.60 Å R-free 0.371
4I3A Structures of PR1 and PR2 intermediates from time-resolved laue crystallography collected at 14ID-B, APS Deposited 2012-11-26	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Not recorded	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；2.6M AMMONIUM SULFATE, 50MM SODIUM PHOSPHATE, pH 7.0, temperature 298K, VAPOR DIFFUSION, HANGING DROP	Resolution 1.60 Å R-free 0.349
4I3I Structures of IT intermediate of photoactive yellow protein E46Q mutant from time-resolved laue crystallography collected at 14ID APS Deposited 2012-11-26	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Mutation：E46Q	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；2.6M AMMONIUM SULFATE, 50MM SODIUM PHOSPHATE, pH 7.0, temperature 298K, VAPOR DIFFUSION, HANGING DROP	Resolution 1.60 Å R-free 0.168
4I3J Structures of PR1 intermediate of photoactive yellow protein E46Q mutant from time-resolved laue crystallography collected AT 14ID APS Deposited 2012-11-26	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Mutation：E46Q	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；2.6M AMMONIUM SULFATE, 50MM SODIUM PHOSPHATE, pH 7.0, temperature 298K, VAPOR DIFFUSION, HANGING DROP	Resolution 1.60 Å R-free 0.321
4WL9 Time Resolved Serial Femtosecond Crystallography Captures High Resolution Intermediates of PYP Deposited 2014-10-06	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Not recorded	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；pH 7；296 K；Microcrystals (~ 2 x 2 x 5 um^3) were formed by centrifugation in a spin filter.	Resolution 1.60 Å R-free 0.231
4WLA Time Resolved Serial Femtosecond Crystallography Captures High Resolution Intermediates of PYP Deposited 2014-10-06	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Not recorded	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；pH 7；296 K；Microcrystals of ~2 x 2 x 5 um3 size were created by centrifugation in spin filters	Resolution 1.60 Å R-free 0.283
5GX9 PYP mutant - E46Q Deposited 2016-09-16	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Mutation：E46Q	HC4 4'-HYDROXYCINNAMIC ACID × 1	NEUTRON DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；295 K；AMMONIUM SULPHATE, SODIUM CHLORIDE, SODIUM DIDEUTERIUM PHOSPHATE, DISODIUM DEUTERIUM PHOSPHATE, pH 9.0, VAPOR DIFFUSION, HANGING DROP, MICROSEEDING, temperature 295K	Resolution 1.49 Å R-free 0.200
5HD3 Femtosecond Structural Dynamics Drives the Trans/Cis Isomerization in Photoactive Yellow Protein: Dark structure of photoactive yellow protein Deposited 2016-01-04	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions LIQUID DIFFUSION；pH 7；295 K；4.45M Sodium malonate (pH7) injected into concentrated protein for a final malonate concentration of 3.2M. Sit for 1 hour at room temperature. Spin in spin concentrator for 2 hours. Sit at room temperature for 4 hours. Crystals are harvested and resuspended in 3.0M malonate.	Resolution 1.60 Å R-free 0.181
5HD5 Femtosecond Structural Dynamics Drives the Trans/Cis Isomerization in Photoactive Yellow Protein: 200 ns time delay photo-activated (light) structure Deposited 2016-01-04	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions LIQUID DIFFUSION；pH 7；295 K；Microcrystalization using combination free interface diffusion and spin centrifugation.	Resolution 1.60 Å R-free 0.374
5HDC Femtosecond Structural Dynamics Drives the Trans/Cis Isomerization in Photoactive Yellow Protein: 100 fs to 400 fs Structure Deposited 2016-01-05	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions LIQUID DIFFUSION；pH 7；295 K；Combine and vortex 4.45M sodium malonate with 100 uL protein (135 mg/ml initial concentration) for a final sodium malonate concentration of 3.2M. Let stand at room temperature for 1 hour. Spin at 10,000g for 2 hours in small spin concentrators. Vortex and let stand at room temperature for 4 hours. Harvest crystals and rebuffer with 3.0M sodium malonate.	Resolution 1.60 Å R-free 0.258
5HDD Femtosecond Structural Dynamics Drives the Trans/Cis Isomerization in Photoactive Yellow Protein: 800 fs to 1200 fs Structure Deposited 2016-01-05	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions LIQUID DIFFUSION；295 K；Combine and vortex 4.45M sodium malonate with 100 uL protein (135 mg/ml initial concentration) for a final sodium malonate concentration of 3.2M. Let stand at room temperature for 1 hour. Spin at 10,000g for 2 hours in small spin concentrators. Vortex and let stand at room temperature for 4 hours. Harvest crystals and rebuffer with 3.0M sodium malonate.	Resolution 1.60 Å R-free 0.265
5HDS Femtosecond Structural Dynamics Drives the Trans/Cis Isomerization in Photoactive Yellow Protein: 3 ps Structure Deposited 2016-01-05	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions LIQUID DIFFUSION；pH 7；295 K；Combine and vortex 4.45M sodium malonate with 100 uL protein (135 mg/ml initial concentration) for a final sodium malonate concentration of 3.2M. Let stand at room temperature for 1 hour. Spin at 10,000g for 2 hours in small spin concentrators. Vortex and let stand at room temperature for 4 hours. Harvest crystals and rebuffer with 3.0M sodium malonate.	Resolution 1.60 Å R-free 0.240
6MHI Photoactive Yellow Protein with covalently bound 3,5-dichloro-4-hydroxycinnamic acid chromophore Deposited 2018-09-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Not recorded	YYZ (2E)-3-(3,5-dichloro-4-hydroxyphenyl)prop-2-enoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；1M sodium chloride, 2.4M ammonium sulfate, pH = 6.0, drops were microseeded	Resolution 1.35 Å R-free 0.186
6MHN Photoactive Yellow Protein with covalently bound 3-chloro-4-hydroxycinnamic acid chromophore Deposited 2018-09-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Not recorded	YAZ (2E)-3-(3-chloro-4-hydroxyphenyl)prop-2-enoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；1M sodium chloride, 2.4M ammonium sulfate, pH = 6.0, drops were microseeded	Resolution 1.67 Å R-free 0.215
6MKT Photoactive Yellow Protein with 3-chlorotyrosine substituted at position 42 Deposited 2018-09-26	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；1M sodium chloride, 2.4M ammonium sulfate, pH = 6.0, drops were microseeded	Resolution 1.60 Å R-free 0.189
6MMD Photoactive Yellow Protein with 3,5-dichlorotyrosine substituted at position 42 Deposited 2018-09-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–125（125 aa） Chain B 1–125（125 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	HC4 4'-HYDROXYCINNAMIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；1M sodium chloride, 2.4M ammonium sulfate, pH = 6.0, drops were microseeded	Resolution 1.23 Å R-free 0.181
6P4I Photoactive Yellow Protein PYP 10ps Deposited 2019-05-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions SMALL TUBES；pH 7；293 K；Sodium Malonate	Resolution 1.60 Å R-free 0.342
6P5D Photoactive Yellow Protein PYP 30ps Deposited 2019-05-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions SMALL TUBES；293 K；Sodium Malonate	Resolution 1.60 Å R-free 0.267
6P5E Photoactive Yellow Protein PYP 80ps Deposited 2019-05-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions SMALL TUBES；293 K；Sodium Malonate	Resolution 1.60 Å R-free 0.326
6P5F Photoactive Yellow Protein PYP Pure Dark Deposited 2019-05-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions SMALL TUBES；293 K；Sodium Malonate	Resolution 1.70 Å R-free 0.241
6P5G Photoactive Yellow Protein PYP Dark Full Deposited 2019-05-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions SMALL TUBES；293 K；Sodium Malonate	Resolution 1.60 Å R-free 0.201
6UMY Crystal structure of photoactive yellow protein (PYP); F96(4-IF) construct Deposited 2019-10-10	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；20 mM potassium phosphate, pH 6.0, 1 M NaCl, 1.9 M ammonium sulfate	Resolution 0.92 Å R-free 0.138
6UMZ Crystal structure of photoactive yellow protein (PYP); 3-Br-p-coumaric acid chromophore Deposited 2019-10-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Not recorded	QBV (2E)-3-(3-bromo-4-hydroxyphenyl)prop-2-enoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；20 mM potassium phosphate, pH 6.0, 1 M NaCl, 1.9 M ammonium sulfate	Resolution 0.90 Å R-free 0.137
6UN0 Crystal structure of photoactive yellow protein (PYP); F96(4-IF) construct with 3-Br-p-coumaric acid chromophore Deposited 2019-10-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	QBV (2E)-3-(3-bromo-4-hydroxyphenyl)prop-2-enoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；20 mM potassium phosphate, pH 6.0, 1 M NaCl; 1.9 M ammonium sulfate	Resolution 0.85 Å R-free 0.133
6UN2 Crystal structure of photoactive yellow protein (PYP); C69U construct (selenocysteine incorporation) Deposited 2019-10-10	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Not recorded	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；20 mM potassium phosphate, pH 6.0, 1 M NaCl, 1.9 M ammonium sulfate	Resolution 0.97 Å R-free 0.157
7AV6 FAST in a domain-swapped dimer form Deposited 2020-11-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–125（125 aa）	Not recorded	FMT FORMIC ACID × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M magnesium formate, 20 % w/v PEG 3350	Resolution 1.50 Å R-free 0.237
7SJJ Crystal structure of photoactive yellow protein (PYP); F96oCNF construct Deposited 2021-10-17	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；20 mM potassium phosphate, pH 6.0, 1 M NaCl; 2.1 M ammonium sulfate	Resolution 0.95 Å R-free 0.159
7SPV Crystal structure of photoactive yellow protein (PYP); F92oCNF construct Deposited 2021-11-03	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；20 mM potassium phosphate, pH 6.0, 1 M NaCl; 2.0 M ammonium sulfate	Resolution 1.18 Å R-free 0.189
7SPW Crystal structure of photoactive yellow protein (PYP); F62oCNF construct Deposited 2021-11-03	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；20 mM potassium phosphate, pH 6.0, 1 M NaCl; 2.4 M ammonium sulfate	Resolution 1.05 Å R-free 0.158
7SPX Crystal structure of photoactive yellow protein (PYP); F28oCNF construct Deposited 2021-11-03	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；20 mM potassium phosphate, pH 6.0, 1 M NaCl; 2.2 M ammonium sulfate	Resolution 0.97 Å R-free 0.166
8AO0 Solution structure of nanoFAST/HBR-DOM2 complex Deposited 2022-08-08	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–125（98 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	O1F (5~{Z})-5-[(2,5-dimethoxy-4-oxidanyl-phenyl)methylidene]-2-sulfanylidene-1,3-thiazolidin-4-one × 1	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) NULL；Pressure AMBIENT NMR sample composition 20 mM NaPi, 20 mM sodium chloride, 0.001 % sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
8DZU Crystal structure of photoactive yellow protein (PYP); F96oCNF M100H construct Deposited 2022-08-08	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；20 mM potassium phosphate, pH 6.0, 1 M NaCl; 2.5 M ammonium sulfate	Resolution 1.04 Å R-free 0.161
8DZX Crystal structure of photoactive yellow protein (PYP); F96oCNF M100K construct Deposited 2022-08-08	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；20 mM potassium phosphate, pH 6.0, 1 M NaCl; 2.5 M ammonium sulfate	Resolution 1.14 Å R-free 0.189
8DZY Crystal structure of photoactive yellow protein (PYP); F96oCNF I49T construct Deposited 2022-08-08	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；20 mM potassium phosphate, pH 6.0, 1 M NaCl; 2.0 M ammonium sulfate	Resolution 1.01 Å R-free 0.161
8E02 Crystal structure of photoactive yellow protein (PYP); F96oCNF T103V construct Deposited 2022-08-08	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；20 mM potassium phosphate, pH 6.0, 1 M NaCl; 2.0 M ammonium sulfate	Resolution 1.09 Å R-free 0.169
8E03 Crystal structure of photoactive yellow protein (PYP); F96oCNF M100D construct Deposited 2022-08-08	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；20 mM potassium phosphate, pH 6.0, 1 M NaCl; 2.4 M ammonium sulfate	Resolution 1.24 Å R-free 0.181
8E09 Crystal structure of photoactive yellow protein (PYP); F96oCNF M100E construct Deposited 2022-08-08	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；20 mM potassium phosphate, pH 6.0, 1 M NaCl; 2.2 M ammonium sulfate	Resolution 1.01 Å R-free 0.164
8E1K Crystal structure of photoactive yellow protein (PYP); F96oCNF M100Q construct Deposited 2022-08-10	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Mutation：M100Q Non-standard monomer：Yes (specific site not provided by mmCIF)	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；20 mM potassium phosphate, pH 6.0, 1 M NaCl; 2.1 M ammonium sulfate	Resolution 1.02 Å R-free 0.161
8E1L Crystal structure of photoactive yellow protein (PYP); F96oCNF M100N construct Deposited 2022-08-10	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Mutation：M100N Non-standard monomer：Yes (specific site not provided by mmCIF)	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；20 mM potassium phosphate, pH 6.0, 1 M NaCl; 2.6 M ammonium sulfate	Resolution 1.20 Å R-free 0.188
9AZ7 Chloride Sites in Photoactive Yellow Protein Deposited 2024-03-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Not recorded	HC4 4'-HYDROXYCINNAMIC ACID × 1 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；293 K；2.2 M ammonium sulfate, 1.0 M sodium chloride, 20 mM sodium phosphate	Resolution 2.00 Å R-free 0.182
9AZ9 Chloride Sites in Photoactive Yellow Protein (Chloride-Free Reference Structure) Deposited 2024-03-10	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Not recorded	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；293 K；2.5 M ammonium sulfate, 1.5 M sodium chloride, 20 mM sodium phosphate, dialyzed against (1) 3.0 M ammonium sulfate, 0.5 M sodium chloride, 20 mM sodium phosphate, then (2) 3.5 M ammonium sulfate, 20 mM sodium phosphate	Resolution 2.00 Å R-free 0.176
9CGH Photoactive yellow protein crystallized in situ on cyclic olefin copolymer microfluidic chip through counter diffusion Deposited 2024-06-28	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Not recorded	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions COUNTER-DIFFUSION；293 K；PEG 4000, 2-Morpholinoethanesulphonic acid	Resolution 1.32 Å R-free 0.179
9D10 Photoactive Yellow Protein, crystals from PEG, room temperature Deposited 2024-08-07	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Not recorded	HC4 4'-HYDROXYCINNAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；pH 6.5；292 K；100 mM MES, 40% PEG 4000	Resolution 1.80 Å R-free 0.198
9O8V Apo Form of Photoactive Yellow Protein Deposited 2025-04-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–125（125 aa） Chain B 1–125（125 aa）	Not recorded	CL CHLORIDE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；Ammonium Sulfate, Sodium chloride, Potassium phosphate	Resolution 1.29 Å R-free 0.185

101 other PDB entries and 103 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PYP_ECTHA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–122； UniProt 4–125

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1d7e
Deposition date deposition_date	1999-10-17
Structure title title	CRYSTAL STRUCTURE OF THE P65 CRYSTAL FORM OF PHOTOACTIVE YELLOW PROTEIN
Keywords keywords	PHOTORECEPTOR, PHOTOSYNTHESIS; PHOTOSYNTHESIS
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	14.58 Å
Radius of gyration Rg (electron density) rg_electron	12.97 Å
Forward intensity I(0) i0	3525700.00
Molecular weight molecular_weight	13388.0 kDa
Excluded volume excluded_volume	16794 Å³
Envelope volume envelope_volume	18117 Å³
Hydration-shell volume shell_volume	11715 Å³
Envelope diameter envelope_diameter	40.8 Å
Shell Rg shell_rg	19.01 Å
Envelope Rg envelope_rg	13.27 Å
Shape Rg shape_rg	12.93 Å
Total Rg total_rg	14.40 Å
Total atoms total_atoms	944
Residues n_residues	120
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	43.7 Å
Rg (real space) rg_real	14.45 Å
Rg uncertainty (real space) rg_real_error	0.16 Å
I(0) (real space) i0_real	3.5260e+06
I(0) uncertainty (real space) i0_real_error	3.5820e+04
Rg (reciprocal space) rg_reciprocal	14.46 Å
I(0) (reciprocal space) i0_reciprocal	3526000.0000
Solution quality estimate total_estimate	0.8997
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.8 Å
Skewness Skewness skewness	0.007
Kurtosis Kurtosis kurtosis	-0.444
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	778600.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.909; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.995

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	PHOTOACTIVE YELLOW PROTEIN
Molecular weight formula_weight	13490.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1104

VAFGSEDIENTLAKMDDGQLDGLAFGAIQLDGDGNILQYNAAEGDITGRDPKQVIGKNFFKDVAPCTDSPEFYGKFKEGVASGNLNTMFEYTFDYQMTPTKVKVHMKKALSGDSYWVFVKRV

来源 Source

来源生物 organism	Halorhodospira halophila
NCBI Class编号 ncbi_taxonomy_id	1053
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	;4'-HYDROXYCINNAMIC ACID ;
Molecular weight formula_weight	164.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	151

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1d7ea_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.110 — Profilin-like
Superfamily Superfamily superfamily	d.110.3 — PYP-like sensor domain (PAS domain)
Family Family family	d.110.3.1 — PYP-like

CATH v4.4 (1 domains)

Domain ID domain_id	1d7eA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	20 — PAS domain

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8. Citations (3)

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Unit-cell length a length_a	40.561 Å
Unit-cell length b length_b	40.561 Å
Unit-cell length c length_c	118.089 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 65
Space-group number int_tables_number	170
Crystal system crystal_system	—

Resolution resolution	1.390 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1390
R_work r_work	0.1390
R_free r_free	0.1980

fit	/app/data/saxs_computation/d7/1d7e/1d7e.fit
pddf	/app/data/pr_computation/d7/1d7e/1d7e.pr.out
profile	/app/data/saxs_computation/d7/1d7e/1d7e.dat