1tro

CRYSTAL STRUCTURE OF TRP REPRESSOR OPERATOR COMPLEX AT ATOMIC RESOLUTION

Method: X-RAY DIFFRACTION D_max: 131.6 Å Quality: REASONABLE

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

PROTEIN (TRP REPRESSOR)

OrganismNot specified

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–DNA Homooligomer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain A； UniProt 0–107 Chain C； UniProt 0–107	Not recorded	;DNA (5'-D(TPGPTPAPCPTPAPGPTPTPAPAPCPTPAPGPT PAPC)-3') ; × 2 TRP* TRYPTOPHAN × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；VAPOR DIFFUSION	Resolution 1.90 Å
2	Protein–DNA Homooligomer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain E； UniProt 0–107 Chain G； UniProt 0–107	Not recorded	;DNA (5'-D(TPGPTPAPCPTPAPGPTPTPAPAPCPTPAPGPT PAPC)-3') ; × 2 TRP* TRYPTOPHAN × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；VAPOR DIFFUSION	Resolution 1.90 Å

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 1TRO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CO0 NMR STUDY OF TRP REPRESSOR-MTR OPERATOR DNA COMPLEX Deposited 1999-05-30	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–107（107 aa） Chain B 1–107（107 aa）	Not recorded	TRP TRYPTOPHAN × 2	SOLUTION NMR NMR measurement conditions pH 5.7	Resolution not provided
1JHG TRP REPRESSOR MUTANT V58I Deposited 1996-07-19	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 7–107（101 aa）	Mutation：CHAIN A, V58I	PO4 PHOSPHATE ION × 2 TRP TRYPTOPHAN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；HANGING DROP VAPOR DIFFUSION 2.0 M SODIUM PHOSPHATE, PH 5.0 600 MM AMMONIUM CHLORIDE 5 MM L-TRYPTOPHAN, vapor diffusion - hanging drop	Resolution 1.30 Å R-free 0.172
1MI7 Crystal Structure of Domain Swapped trp Aporepressor in 30%(v/v) Isopropanol Deposited 2002-08-22	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 R 1–107（107 aa）	Not recorded	IPA ISOPROPYL ALCOHOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；100 mM Na HEPES, 100 mM sodium chloride, 30%(v/v) isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.50 Å R-free 0.288
1RCS NMR STUDY OF TRP REPRESSOR-OPERATOR DNA COMPLEX Deposited 1995-05-12	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 3–106（104 aa） Chain B 3–106（104 aa）	Not recorded	TRP TRYPTOPHAN × 2	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1TRR TANDEM BINDING IN CRYSTALS OF A TRP REPRESSOR/OPERATOR HALF-SITE COMPLEX Deposited 1993-10-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric	Chain A 1–107（107 aa） Chain B 1–107（107 aa） Chain G 1–107（107 aa） Chain H 1–107（107 aa）	Not recorded	TRP TRYPTOPHAN × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å
1TRR TANDEM BINDING IN CRYSTALS OF A TRP REPRESSOR/OPERATOR HALF-SITE COMPLEX Deposited 1993-10-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric	Chain D 1–107（107 aa） Chain E 1–107（107 aa） Chain J 1–107（107 aa） Chain K 1–107（107 aa）	Not recorded	TRP TRYPTOPHAN × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å
1WRP FLEXIBILITY OF THE DNA-BINDING DOMAINS OF TRP REPRESSOR Deposited 1987-12-01	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain R 1–107（107 aa）	Not recorded	TRP TRYPTOPHAN × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å
1WRS NMR STUDY OF HOLO TRP REPRESSOR Deposited 1995-05-12	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain R 3–107（105 aa） Chain S 3–107（105 aa）	Not recorded	TRP TRYPTOPHAN × 2	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1WRT NMR STUDY OF APO TRP REPRESSOR Deposited 1995-05-12	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain R 3–107（105 aa） Chain S 3–107（105 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1ZT9 E. coli trp repressor, tetragonal crystal form Deposited 2005-05-26	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 1–107（107 aa） Chain B 1–107（107 aa）	Not recorded	SO4 SULFATE ION × 4 TRP TRYPTOPHAN × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；294 K；2.8 M ammonium sulfate plus 50 mM sodium, potassium phosphate buffer, 5 mM L-tryptophan, VAPOR DIFFUSION, HANGING DROP, temperature 294K, pH 5.60	Resolution 2.00 Å R-free 0.219
1ZT9 E. coli trp repressor, tetragonal crystal form Deposited 2005-05-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain D 1–107（107 aa） Chain E 1–107（107 aa）	Not recorded	SO4 SULFATE ION × 4 TRP TRYPTOPHAN × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；294 K；2.8 M ammonium sulfate plus 50 mM sodium, potassium phosphate buffer, 5 mM L-tryptophan, VAPOR DIFFUSION, HANGING DROP, temperature 294K, pH 5.60	Resolution 2.00 Å R-free 0.219
1ZT9 E. coli trp repressor, tetragonal crystal form Deposited 2005-05-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–107（107 aa） Chain B 1–107（107 aa） Chain D 1–107（107 aa） Chain E 1–107（107 aa）	Not recorded	SO4 SULFATE ION × 8 TRP TRYPTOPHAN × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；294 K；2.8 M ammonium sulfate plus 50 mM sodium, potassium phosphate buffer, 5 mM L-tryptophan, VAPOR DIFFUSION, HANGING DROP, temperature 294K, pH 5.60	Resolution 2.00 Å R-free 0.219
1ZT9 E. coli trp repressor, tetragonal crystal form Deposited 2005-05-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–107（107 aa） Chain B 1–107（107 aa） Chain D 1–107（107 aa） Chain E 1–107（107 aa）	Not recorded	SO4 SULFATE ION × 8 TRP TRYPTOPHAN × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；294 K；2.8 M ammonium sulfate plus 50 mM sodium, potassium phosphate buffer, 5 mM L-tryptophan, VAPOR DIFFUSION, HANGING DROP, temperature 294K, pH 5.60	Resolution 2.00 Å R-free 0.219
1ZT9 E. coli trp repressor, tetragonal crystal form Deposited 2005-05-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–107（107 aa） Chain B 1–107（107 aa） Chain D 1–107（107 aa） Chain E 1–107（107 aa）	Not recorded	SO4 SULFATE ION × 8 TRP TRYPTOPHAN × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；294 K；2.8 M ammonium sulfate plus 50 mM sodium, potassium phosphate buffer, 5 mM L-tryptophan, VAPOR DIFFUSION, HANGING DROP, temperature 294K, pH 5.60	Resolution 2.00 Å R-free 0.219
2OZ9 E. coli TRP holorepressor, orthorhombic crystal form Deposited 2007-02-25	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 R 2–108（107 aa）	Not recorded	NA SODIUM ION × 2 SO4 SULFATE ION × 2 TRP TRYPTOPHAN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5；298 K；crystallization conditions: 2.5 M sodium phosphate, 0.6 M ammonium chloride, 2.5 mM L-tryptophan. Prior to data collection the crystal was equilibrated to 2.4 M ammonium sulfate, 0.4 M sodium chloride, 2.4 mM L-tryptophan, 50 mM sodium acetate., pH 5.0, VAPOR DIFFUSION, temperature 298K	Resolution 1.65 Å
3SSW E. coli trp aporepressor Deposited 2011-07-08	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 N 2–108（107 aa） Chain R 2–108（107 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；294 K；Hampton Research Crystal Screen condition #6: 30% (w/v) PEG 4000, 200 mM MgCl2, 100 mM Tris HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 1.67 Å R-free 0.219
3SSX E. coli trp aporeporessor L75F mutant Deposited 2011-07-08	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 N 2–108（107 aa） Chain R 2–108（107 aa）	Mutation：L75F Mutation：L75F	TAM TRIS(HYDROXYETHYL)AMINOMETHANE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；294 K；Hampton Research Crystal Screen condition #6: 30% (w/v) PEG 4000, 200 mM MgCl2, 100 mM Tris HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 1.58 Å R-free 0.218
3WRP FLEXIBILITY OF THE DNA-BINDING DOMAINS OF TRP REPRESSOR Deposited 1987-12-01	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 1–107（107 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å
6EJW Tryptophan Repressor TrpR from E.coli wildtype with Indole-3-acetic acid as ligand Deposited 2017-09-23	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 1–108（108 aa） Chain B 1–108（108 aa）	Not recorded	IAC 1H-INDOL-3-YLACETIC ACID × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.1 M Bis-Tris pH 5.5 2 M Ammonium sulfate	Resolution 1.99 Å R-free 0.243
6EJW Tryptophan Repressor TrpR from E.coli wildtype with Indole-3-acetic acid as ligand Deposited 2017-09-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–108（108 aa） Chain D 1–108（108 aa）	Not recorded	IAC 1H-INDOL-3-YLACETIC ACID × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.1 M Bis-Tris pH 5.5 2 M Ammonium sulfate	Resolution 1.99 Å R-free 0.243
6EKP Tryptophan Repressor TrpR from E.coli variant T44L T81M S88Y with Indole-3-acetic acid as ligand Deposited 2017-09-26	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 1–108（108 aa） Chain B 1–108（108 aa）	Not recorded	IAC 1H-INDOL-3-YLACETIC ACID × 2 P3G 3,6,9,12,15-PENTAOXAHEPTADECANE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.05 Calcium Chloride 0.1M Bis-Tris pH 6.5 30% PEG 550 MME	Resolution 1.46 Å R-free 0.190
6ELB Tryptophan Repressor TrpR from E.coli variant M42F T44L T81M N87G S88Y with Indole-3-acetic acid as ligand Deposited 2017-09-28	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 1–108（108 aa） Chain B 1–108（108 aa）	Not recorded	IAC 1H-INDOL-3-YLACETIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；25% PEG 3350 0.17M KCl 3% D-(+) Trehalose dihydrate	Resolution 1.44 Å R-free 0.193
6ELF Tryptophan Repressor TrpR from E.coli variant M42F T44L T81I S88Y with Indole-3-acetic acid as ligand Deposited 2017-09-28	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 1–108（108 aa） Chain B 1–108（108 aa）	Not recorded	IAC 1H-INDOL-3-YLACETIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1M MES pH 6.5 12 % PEG 20000	Resolution 1.83 Å R-free 0.217
6ELG Tryptophan Repressor TrpR from E.coli variant M42F T44L T81I S88Y with Indole-3-acetonitrile Deposited 2017-09-28	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 1–108（108 aa） Chain B 1–108（108 aa）	Not recorded	3BO 1H-indol-3-ylacetonitrile × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.2 M Ammonium Formate 20% PEG 3350	Resolution 1.38 Å R-free 0.176
6ENI Tryptophan Repressor TrpR from E.coli variant T44L S88Y with Indole-3-acetic acid as ligand Deposited 2017-10-04	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 1–108（108 aa） Chain B 1–108（108 aa）	Not recorded	IAC 1H-INDOL-3-YLACETIC ACID × 2 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；293 K；0.1 M MMT buffer pH 4 25 % PEG 1500	Resolution 1.10 Å R-free 0.175
6ENN Tryptophan Repressor TrpR from E.coli variant T44L T81M N87G S88Y with Indole-3-acetic acid as ligand Deposited 2017-10-05	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 1–108（108 aa） Chain B 1–108（108 aa）	Not recorded	IAC 1H-INDOL-3-YLACETIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；0.1 M MMT buffer pH 5 25 % PEG 1500	Resolution 1.17 Å R-free 0.180
6F7F Tryptophan Repressor TrpR from E.coli with 3-Indolepropionic acid Deposited 2017-12-08	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 4–106（103 aa） Chain B 4–106（103 aa）	Not recorded	IOP INDOLYLPROPIONIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.2 M Calcium Chloride 0.1 M HEPES pH7.5 30% PEG 4000	Resolution 2.13 Å R-free 0.229
6F7F Tryptophan Repressor TrpR from E.coli with 3-Indolepropionic acid Deposited 2017-12-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 4–106（103 aa） Chain D 4–106（103 aa）	Not recorded	IOP INDOLYLPROPIONIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.2 M Calcium Chloride 0.1 M HEPES pH7.5 30% PEG 4000	Resolution 2.13 Å R-free 0.229
6F7G Tryptophan Repressor TrpR from E.coli with 5-Methyltryptamine Deposited 2017-12-08	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 4–106（103 aa） Chain C 4–106（103 aa）	Not recorded	CVW 2-(5-methyl-1~{H}-indol-3-yl)ethanamine × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 Sodium Chloride 0.1 M HEPES pH7.5 25% PEG 3350	Resolution 1.66 Å R-free 0.226
6F9K Tryptophan Repressor TrpR from E.coli with 5-methyl-L-tryptophan as ligand Deposited 2017-12-14	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 1–107（107 aa）	Not recorded	D0Q 5-methyl-L-tryptophan × 8 SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；293 K；0.1M Citric acid pH3.5, 2.4M Ammonium sulfate, pH4.0 cryo: +25% glycerol	Resolution 1.40 Å R-free 0.206
6FAL Tryptophan Repressor TrpR from E.coli with 3-Indolepropionic acid as ligand Deposited 2017-12-15	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 2–108（107 aa） Chain B 2–108（107 aa）	Not recorded	IOP INDOLYLPROPIONIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.2M MgCl2 0.1M Tris HCl, pH8.5 30% PEG 4000	Resolution 1.20 Å R-free 0.179
6ST6 Crystal Structure of Domain Swapped Trp Repressor V58I Variant Deposited 2019-09-10	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 1–105（105 aa）	Mutation：V58I	IPA ISOPROPYL ALCOHOL × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；100 mM Na HEPES, 100 mM sodium chloride, 27.5-35%(v/v) isopropanol, pH 7.5	Resolution 2.05 Å R-free 0.311
6ST7 Crystal Structure of Domain Swapped Trp Repressor V58I Variant with bound L-trp Deposited 2019-09-10	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 1–105（105 aa）	Mutation：V58I	TRP TRYPTOPHAN × 2 IPA ISOPROPYL ALCOHOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；100 mM Na HEPES, 100 mM sodium chloride, 27.5-35%(v/v) isopropanol, pH 7.5	Resolution 2.45 Å R-free 0.287

26 other PDB entries and 33 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TRPR_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–108； UniProt 0–107 Author chain C； PDBConstruct 1–108； UniProt 0–107 Author chain E； PDBConstruct 1–108； UniProt 0–107 Author chain G； PDBConstruct 1–108； UniProt 0–107

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	1tro
Deposition date deposition_date	1992-08-30
Structure title title	CRYSTAL STRUCTURE OF TRP REPRESSOR OPERATOR COMPLEX AT ATOMIC RESOLUTION
Keywords keywords	PROTEIN-DNA COMPLEX, DOUBLE HELIX, TRANSCRIPTION-DNA COMPLEX; TRANSCRIPTION/DNA
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	37.03 Å
Radius of gyration Rg (electron density) rg_electron	37.18 Å
Forward intensity I(0) i0	109309000.00
Molecular weight molecular_weight	69537.0 kDa
Excluded volume excluded_volume	80748 Å³
Envelope volume envelope_volume	117700 Å³
Hydration-shell volume shell_volume	28232 Å³
Envelope diameter envelope_diameter	127.7 Å
Shell Rg shell_rg	40.13 Å
Envelope Rg envelope_rg	36.65 Å
Shape Rg shape_rg	37.14 Å
Total Rg total_rg	37.43 Å
Total atoms total_atoms	4801
Residues n_residues	477
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	131.6 Å
Rg (real space) rg_real	37.60 Å
Rg uncertainty (real space) rg_real_error	1.67 Å
I(0) (real space) i0_real	1.0930e+08
I(0) uncertainty (real space) i0_real_error	2.0380e+06
Rg (reciprocal space) rg_reciprocal	37.25 Å
I(0) (reciprocal space) i0_reciprocal	109300000.0000
Solution quality estimate total_estimate	0.7386
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	27.5 Å
Skewness Skewness skewness	0.536
Kurtosis Kurtosis kurtosis	-0.567
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7082000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.493; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.252; Smooth: 0.868

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	;DNA (5'-D(TPGPTPAPCPTPAPGPTPTPAPAPCPTPAPGPT PAP*C)-3') ;
Molecular weight formula_weight	5818.8 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I,J,K,L
Atom count atom_count	5373

TGTACTAGTTAACTAGTAC

Entity 2 Entity 2 polymer

Description description	PROTEIN (TRP REPRESSOR)
Molecular weight formula_weight	12371.1 kDa
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G

MAQQSPYSAAMAEERHQEWLRFVDLLKNAYQNDLHLPLLNLMLTPDEREALGTRVRIVEELLRGEMSQRELKNELGAGIATITRGSNSLKAAPVELRQWLEEVLLKSD

Entity 3 Entity 3 non-polymer

Description description	TRYPTOPHAN
Molecular weight formula_weight	204.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	572

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1troa_
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.12 — TrpR-like
Family Family family	a.4.12.1 — Trp repressor, TrpR

Domain ID domain_id	d1troc_
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.12 — TrpR-like
Family Family family	a.4.12.1 — Trp repressor, TrpR

Domain ID domain_id	d1troe_
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.12 — TrpR-like
Family Family family	a.4.12.1 — Trp repressor, TrpR

Domain ID domain_id	d1trog_
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.12 — TrpR-like
Family Family family	a.4.12.1 — Trp repressor, TrpR

CATH v4.4 (4 domains)

Domain ID domain_id	1troA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1270 — Trp Operon Repressor; Chain A
Homologous superfamily homologous superfamily	10 — TrpR-like

Domain ID domain_id	1troC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1270 — Trp Operon Repressor; Chain A
Homologous superfamily homologous superfamily	10 — TrpR-like

Domain ID domain_id	1troE00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1270 — Trp Operon Repressor; Chain A
Homologous superfamily homologous superfamily	10 — TrpR-like

Domain ID domain_id	1troG00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1270 — Trp Operon Repressor; Chain A
Homologous superfamily homologous superfamily	10 — TrpR-like

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8. Citations (2)

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Unit-cell length a length_a	43.650 Å
Unit-cell length b length_b	72.430 Å
Unit-cell length c length_c	107.390 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.96 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1670
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/tr/1tro/1tro.fit
pddf	/app/data/pr_computation/tr/1tro/1tro.pr.out
profile	/app/data/saxs_computation/tr/1tro/1tro.dat

CRYSTAL STRUCTURE OF TRP REPRESSOR OPERATOR COMPLEX AT ATOMIC RESOLUTION

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

PROTEIN (TRP REPRESSOR)

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)