5y23

X-ray crystal structure of Pseudoazurin Met16Phe variant

Method: X-RAY DIFFRACTION D_max: 65.8 Å Quality: GOOD

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

Pseudoazurin

Achromobacter cycloclastes

UniProt P19567

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 29–152	Mutation：M16F	CU COPPER (II) ION × 1 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；Drop: 100 mM Tris-HCl buffer, 15.5 % PEG4000, 31 mg/mL Protein Reservoir: 100 mM Tris-HCl buffer, 31 % PEG4000	Resolution 1.40 Å R-free 0.182
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 29–152	Mutation：M16F	CU COPPER (II) ION × 1 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；Drop: 100 mM Tris-HCl buffer, 15.5 % PEG4000, 31 mg/mL Protein Reservoir: 100 mM Tris-HCl buffer, 31 % PEG4000	Resolution 1.40 Å R-free 0.182

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 5Y23	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BQK OXIDIZED PSEUDOAZURIN Deposited 1998-08-17	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 29–152（124 aa）	Not recorded	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6.0	Resolution 1.35 Å R-free 0.190
1BQR REDUCED PSEUDOAZURIN Deposited 1998-08-17	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 29–152（124 aa）	Not recorded	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6.0	Resolution 1.60 Å R-free 0.211
1ZIA OXIDIZED PSEUDOAZURIN Deposited 1996-04-09	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 29–152（124 aa）	Not recorded	CU COPPER (II) ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.54 Å
1ZIB REDUCED PSEUDOAZURIN Deposited 1996-04-09	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 29–152（124 aa）	Not recorded	CU COPPER (II) ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å
2JKW Pseudoazurin M16F Deposited 2008-09-01	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 29–152（124 aa）	Mutation：YES	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；5 MM TRIS PH 7.5, 35 % PEG 4000	Resolution 1.60 Å R-free 0.180
2JKW Pseudoazurin M16F Deposited 2008-09-01	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 29–152（124 aa）	Mutation：YES	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；5 MM TRIS PH 7.5, 35 % PEG 4000	Resolution 1.60 Å R-free 0.180
2UX6 Pseudoazurin with engineered amicyanin ligand loop, oxidized form, pH 7.5 Deposited 2007-03-27	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 29–109（81 aa） Chain A 114–152（39 aa）	Not recorded	CU COPPER (II) ION × 1 GOL GLYCEROL × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP VAPOR DIFFUSION METHOD, MIXING 1MICRO-L OF PROTEIN (20 MG/ML IN 50 MM TRIS/HCL, PH 7.5 PLUS 30 MM NACL) WITH 1 MICRO-L RESERVOIR SOLUTION (10 MM TRIS/HCL, PH 7.5 PLUS 2 M AMMONIUM SULFATE PLUS 2 M NACL).	Resolution 1.30 Å R-free 0.226
2UX7 Pseudoazurin with engineered amicyanin ligand loop, reduced form, pH 7.5 Deposited 2007-03-27	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 29–109（81 aa） Chain A 114–152（39 aa）	Not recorded	CU COPPER (II) ION × 1 GOL GLYCEROL × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP VAPOR DIFFUSION METHOD, 1 MICRO-L OF PROTEIN (20MG/ML IN 50 MM TRIS/HCL PLUS 30 MM NACL) WERE MIXED WITH 1 MICRO-L RESORVOIR SOLUTION (10 MM TRIS/HCL PLUS 2 M AMMONIUM SULFATE AND 2 M NACL). THE CRYSTALS WERE REDUCED BY ADDING 50 MM MERCAPTOETHANOL TO THE RESERVOIR SOLUTION AND BECAME COLORLESS AFTER 3 HOURS., pH 7.5	Resolution 1.30 Å R-free 0.201
2UXF Pseudoazurin with engineered amicyanin ligand loop, oxidized form, pH 5.5 Deposited 2007-03-28	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 29–109（81 aa） Chain A 114–152（39 aa）	Not recorded	CU COPPER (II) ION × 1 GOL GLYCEROL × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；HANGING DROP VAPOR DIFFUSION METHOD, 1 MICRO-L PROTEIN (20 MG/ML IN 100 MM MES, PH 5.5 PLUS 30 MM NACL) MIXED WITH 1 MICRO-L OF RESERVOIR SOLUTION (100 MM MES, PH 5.5 PLUS 2 M AMMONIUM SULFATE AND 2 M NACL)	Resolution 2.00 Å R-free 0.204
2UXG Pseudoazurin with engineered amicyanin ligand loop, reduced form, pH 5.5 Deposited 2007-03-28	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 29–109（81 aa） Chain A 114–152（39 aa）	Not recorded	CU COPPER (II) ION × 1 GOL GLYCEROL × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；HANGING DROP VAPOR DIFFUSION METHOD, 1 MICRO-LITER OF PROTEIN (20 MG/ML IN 100 MM MES, PH 5.5 PLUS 30 MM NACL) WAS MIXED WITH 1 MICO-L OF RESERVOIR SOLUTION (100 MM MES, PH 5.5 PLUS 2 M AMMONIUM SULFATE AND 2 M NACL). THE CRYSTALS WERE REDUCED BY ADDING 50 MM MERCAPTOETHANOL TO THE RESERVOIR SOLUTION AND BECAME COLORLESS AFTER 3 HOURS.	Resolution 1.99 Å R-free 0.230
4YL4 1.1 Angstrom resolution X-ray Crystallographic Structure of Psudoazurin Deposited 2015-03-05	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–152（124 aa）	Not recorded	CU COPPER (II) ION × 1 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；30% PEG 4000, 0.1 M Tris, 0.1M magnesium chloride, 5% Glycerol	Resolution 1.10 Å R-free 0.186
5XMO X-ray crystal structure of Pseudoazurin Met16Phe/Thr36Lys variant Deposited 2017-05-16	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 29–152（124 aa）	Mutation：M16F, T36K	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；Buffer for crystallization: 0.1 M sodium acetate pH 4.5 Precipitant: 30 % PEG1500 Soaking (Cryoprotectant): 0.1 M Tris-HCl pH 7.5, 40 % PEG1500	Resolution 1.19 Å R-free 0.161
5YSG X-ray Crystal Structure of Pseudoazurin Met16Gly Variant, Reduced Form. Deposited 2017-11-14	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 29–152（124 aa）	Mutation：M16G	CU COPPER (II) ION × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；30 % PEG1000, 0.1 M Tris-HCl	Resolution 2.00 Å R-free 0.203
5YSG X-ray Crystal Structure of Pseudoazurin Met16Gly Variant, Reduced Form. Deposited 2017-11-14	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 29–152（124 aa）	Mutation：M16G	CU COPPER (II) ION × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；30 % PEG1000, 0.1 M Tris-HCl	Resolution 2.00 Å R-free 0.203
5YSG X-ray Crystal Structure of Pseudoazurin Met16Gly Variant, Reduced Form. Deposited 2017-11-14	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 29–152（124 aa）	Mutation：M16G	CU COPPER (II) ION × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；30 % PEG1000, 0.1 M Tris-HCl	Resolution 2.00 Å R-free 0.203
5YSG X-ray Crystal Structure of Pseudoazurin Met16Gly Variant, Reduced Form. Deposited 2017-11-14	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 29–152（124 aa）	Mutation：M16G	CU COPPER (II) ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；30 % PEG1000, 0.1 M Tris-HCl	Resolution 2.00 Å R-free 0.203
5YW3 X-ray Crystal Structure of Pseudoazurin Thr36Lys Variant Deposited 2017-11-28	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 29–152（124 aa）	Mutation：T36K	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；100mM Tris-HCl, 38% PEG4000, 40mg/mL protein	Resolution 1.19 Å R-free 0.173
5YW3 X-ray Crystal Structure of Pseudoazurin Thr36Lys Variant Deposited 2017-11-28	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 29–152（124 aa）	Mutation：T36K	CU COPPER (II) ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；100mM Tris-HCl, 38% PEG4000, 40mg/mL protein	Resolution 1.19 Å R-free 0.173
5YW3 X-ray Crystal Structure of Pseudoazurin Thr36Lys Variant Deposited 2017-11-28	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 29–152（124 aa）	Mutation：T36K	CU COPPER (II) ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；100mM Tris-HCl, 38% PEG4000, 40mg/mL protein	Resolution 1.19 Å R-free 0.173
5YW3 X-ray Crystal Structure of Pseudoazurin Thr36Lys Variant Deposited 2017-11-28	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 29–152（124 aa）	Mutation：T36K	CU COPPER (II) ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；100mM Tris-HCl, 38% PEG4000, 40mg/mL protein	Resolution 1.19 Å R-free 0.173
5Z0X X-ray Crystal Structure of Pseudoazurin Met16Tyr Variant Deposited 2017-12-22	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 29–152（124 aa）	Mutation：M16Y	CU COPPER (II) ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.1M Tris-HCl, 34% PEG4000, 45mg/mL Protein	Resolution 1.46 Å R-free 0.191
5Z0X X-ray Crystal Structure of Pseudoazurin Met16Tyr Variant Deposited 2017-12-22	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 29–152（124 aa）	Mutation：M16Y	CU COPPER (II) ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.1M Tris-HCl, 34% PEG4000, 45mg/mL Protein	Resolution 1.46 Å R-free 0.191
5ZTD X-ray Crystal Structure of Pseudoazurin Met16Val Variant Deposited 2018-05-02	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 29–152（124 aa） Fragment：UNP residues 29-152	Mutation：M16V	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；Reservoir: 0.1M Tris-HCl (pH 8.5), 27% PEG1000 Drop: 42mg/mL Met16Val Pseudoazurin, 0.1M Tris-HCl (pH 8.5), 13.5% PEG1000	Resolution 1.05 Å R-free 0.151
5ZTD X-ray Crystal Structure of Pseudoazurin Met16Val Variant Deposited 2018-05-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 29–152（124 aa） Fragment：UNP residues 29-152	Mutation：M16V	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；Reservoir: 0.1M Tris-HCl (pH 8.5), 27% PEG1000 Drop: 42mg/mL Met16Val Pseudoazurin, 0.1M Tris-HCl (pH 8.5), 13.5% PEG1000	Resolution 1.05 Å R-free 0.151
6AKN X-ray Crystal Structure of Pseudoazurin Met16Leu Variant Deposited 2018-09-03	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 29–152（124 aa） Fragment：UNP residues 29-152	Mutation：M16L	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1M Tris-HCl (pH 7.5), 32 % PEG4000	Resolution 1.19 Å R-free 0.130
6AKN X-ray Crystal Structure of Pseudoazurin Met16Leu Variant Deposited 2018-09-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 29–152（124 aa） Fragment：UNP residues 29-152	Mutation：M16L	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1M Tris-HCl (pH 7.5), 32 % PEG4000	Resolution 1.19 Å R-free 0.130
6IFP X-ray Crystal Structure of Pseudoazurin Met16Ile Variant Deposited 2018-09-20	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 29–152（124 aa） Fragment：UNP residues 29-152	Mutation：M16I	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M Tris-HCl, 35 % PEG4000	Resolution 1.00 Å R-free 0.144
6IFP X-ray Crystal Structure of Pseudoazurin Met16Ile Variant Deposited 2018-09-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 29–152（124 aa） Fragment：UNP residues 29-152	Mutation：M16I	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M Tris-HCl, 35 % PEG4000	Resolution 1.00 Å R-free 0.144
8HM9 X-ray Crystal Structure of Pseudoazurin Met16His Variant at pH 4.0 Deposited 2022-12-02	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 29–152（124 aa）	Mutation：M16H	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；298 K；31% PEG1500, 0.1 M potassium phosphate (pH 4.0)	Resolution 1.36 Å R-free 0.160
8HM9 X-ray Crystal Structure of Pseudoazurin Met16His Variant at pH 4.0 Deposited 2022-12-02	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 29–152（124 aa）	Mutation：M16H	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；298 K；31% PEG1500, 0.1 M potassium phosphate (pH 4.0)	Resolution 1.36 Å R-free 0.160
8WQZ X-ray Crystal Structure of Pseudoazurin Met16Gly variant Deposited 2023-10-12	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 29–152（124 aa）	Not recorded	CU COPPER (II) ION × 1 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M HEPES, 42 %(w/v) PEG200	Resolution 1.20 Å R-free 0.153
9M62 X-ray Crystal Structure of Pseudoazurin Met16Arg variant, oxidized form at pH 7.0 Deposited 2025-03-06	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 29–152（124 aa）	Mutation：M16R	CU COPPER (II) ION × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；PEG1500, 100 mM potassium phosphate	Resolution 1.22 Å R-free 0.211
9M62 X-ray Crystal Structure of Pseudoazurin Met16Arg variant, oxidized form at pH 7.0 Deposited 2025-03-06	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 29–152（124 aa）	Mutation：M16R	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；PEG1500, 100 mM potassium phosphate	Resolution 1.22 Å R-free 0.211

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

View Construct and Data Evidence

UniProt name	AZUP_ACHCY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–124； UniProt 29–152 Author chain B； PDBConstruct 1–124； UniProt 29–152

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	5y23
Deposition date deposition_date	2017-07-23
Structure title title	X-ray crystal structure of Pseudoazurin Met16Phe variant
Keywords keywords	Electron transfer, Cupredoxin, ELECTRON TRANSPORT; ELECTRON TRANSPORT
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	20.38 Å
Radius of gyration Rg (electron density) rg_electron	19.67 Å
Forward intensity I(0) i0	12448700.00
Molecular weight molecular_weight	26614.0 kDa
Excluded volume excluded_volume	33358 Å³
Envelope volume envelope_volume	38854 Å³
Hydration-shell volume shell_volume	17147 Å³
Envelope diameter envelope_diameter	68.8 Å
Shell Rg shell_rg	24.99 Å
Envelope Rg envelope_rg	19.56 Å
Shape Rg shape_rg	19.64 Å
Total Rg total_rg	20.52 Å
Total atoms total_atoms	1861
Residues n_residues	247
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	65.8 Å
Rg (real space) rg_real	20.37 Å
Rg uncertainty (real space) rg_real_error	0.48 Å
I(0) (real space) i0_real	1.2450e+07
I(0) uncertainty (real space) i0_real_error	1.7820e+05
Rg (reciprocal space) rg_reciprocal	20.37 Å
I(0) (reciprocal space) i0_reciprocal	12450000.0000
Solution quality estimate total_estimate	0.8227
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.5 Å
Skewness Skewness skewness	0.294
Kurtosis Kurtosis kurtosis	-0.518
Angular range angular_range	— – 0.3900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1761000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.905; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.000

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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	Pseudoazurin
Molecular weight formula_weight	13048.9 kDa
Mutation mutation	M16F
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2348

ADFEVHMLNKGKDGAFVFEPASLKVAPGDTVTFIPTDKGHNVETIKGMIPDGAEAFKSKINENYKVTFTAPGVYGVKCTPHYGMGMVGVVQVGDAPANLEAVKGAKNPKKAQERLDAALAALGN

来源 Source

来源生物 organism	Achromobacter cycloclastes
NCBI Class编号 ncbi_taxonomy_id	223
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	COPPER (II) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	318

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5y23a_
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.1 — Plastocyanin/azurin-like

Domain ID domain_id	d5y23b_
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.1 — Plastocyanin/azurin-like

CATH v4.4 (2 domains)

Domain ID domain_id	5y23A00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	5y23B00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

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8. Citations (1)

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Unit-cell length a length_a	34.715 Å
Unit-cell length b length_b	59.620 Å
Unit-cell length c length_c	54.324 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.37 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.400 Å
Low-resolution limit resolution_low	26.200 Å
R factor r_factor	0.1430
R_work r_work	0.1410
R_free r_free	0.1816

fit	/app/data/saxs_computation/y2/5y23/5y23.fit
pddf	/app/data/pr_computation/y2/5y23/5y23.pr.out
profile	/app/data/saxs_computation/y2/5y23/5y23.dat