SAXSdb — 3nyk

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

Pseudoazurin

Alcaligenes faecalis

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 24–146	Not recorded	CO COBALT (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.7；Protein at 5 mg/ml concentration. 50mM Na-citrate pH 5.7, 20 mM CoCl2, 2.8 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP	Resolution 1.86 Å R-free 0.178

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 3NYK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1PAZ REFINEMENT OF THE STRUCTURE OF PSEUDOAZURIN FROM ALCALIGENES FAECALIS S-6 AT 1.55 ANGSTROMS RESOLUTION Deposited 1988-06-28	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 24–146（123 aa）	Not recorded	CU COPPER (II) ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.55 Å
1PY0 Crystal structure of E51C/E54C Psaz from A.faecalis with CLaNP probe Deposited 2003-07-07	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 24–146（123 aa）	Mutation：E51C, E54C	ZN ZINC ION × 1 Y1 YTTRIUM ION × 1 SO4 SULFATE ION × 1 YMA 7,10,13-TRI(CARBOXYMETHYL)-5,15-DIOXO-4,7,10,13,16-PENTAAZA-1,19-DITHIANONADECANE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；2.4M ammonium sulfate, 50mM sodium phosphate buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.00 Å R-free 0.232
1PZA THE CRYSTAL STRUCTURES OF REDUCED PSEUDOAZURIN FROM ALCALIGENES FAECALIS S-6 AT TWO PH VALUES Deposited 1994-09-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 24–146（123 aa）	Not recorded	CU COPPER (II) ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å
1PZB THE CRYSTAL STRUCTURES OF REDUCED PSEUDOAZURIN FROM ALCALIGENES FAECALIS S-6 AT TWO PH VALUES Deposited 1994-08-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 24–146（123 aa）	Not recorded	CU COPPER (II) ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å
1PZC APO-PSEUDOAZURIN (METAL FREE PROTEIN) Deposited 1995-02-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 24–146（123 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.7；pH 6.7	Resolution 1.85 Å R-free 0.215
2P80 Solution structure of the complex between nitrite reductase and pseudoazurin from A. faecalis Deposited 2007-03-21	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 24–146（123 aa）	Not recorded	CU COPPER (II) ION × 7 GD GADOLINIUM ATOM × 9	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 50 mM phosphate；Pressure 1 NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 50 mM phosphate；Pressure 1 NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 50 mM phosphate；Pressure 1 NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 50 mM phosphate；Pressure 1 NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 50 mM phosphate；Pressure 1 NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 50 mM phosphate；Pressure 1 NMR sample composition 250 mM 15N, 2H pseudoazurin in complex with nitrite reductase -bound GdCLaNP at position 221/223 (0.38 eq), in 50 mM phosphate buffer, H2O, 6% (v/v) D2O \| H2O, 6% (v/v) D2O NMR sample composition 250 mM 15N, 2H pseudoazurin in complex with nitrite reductase -bound YCLaNP at position 221/223 (0.38 eq), in 50 mM phosphate buffer, H2O, 6% (v/v) D2O \| H2O, 6% (v/v) D2O NMR sample composition 250 mM 15N, 2H pseudoazurin in complex with nitrite reductase -bound GdCLaNP at position 234/236 (0.32 eq), in 50 mM phosphate buffer, H2O, 6% (v/v) D2O \| H2O, 6% (v/v) D2O NMR sample composition 250 mM 15N, 2H pseudoazurin in complex with nitrite reductase -bound YCLaNP at position 234/236 (0.32 eq), in 50 mM phosphate buffer, H2O, 6% (v/v) D2O \| H2O, 6% (v/v) D2O NMR sample composition 250 mM 15N, 2H pseudoazurin in complex with nitrite reductase -bound GdCLaNP at position 333/336 (0.53 eq), in 50 mM phosphate buffer, H2O, 6% (v/v) D2O \| H2O, 6% (v/v) D2O NMR sample composition 250 mM 15N, 2H pseudoazurin in complex with nitrite reductase -bound YCLaNP at position 333/336 (0.53 eq), in 50 mM phosphate buffer, H2O, 6% (v/v) D2O \| H2O, 6% (v/v) D2O	Resolution not provided
3PAZ REDUCED NATIVE PSEUDOAZURIN FROM A. FAECALIS Deposited 1997-02-20	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 24–146（123 aa）	Not recorded	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；50MM SODIUM PHOSPHATE WITH 75% SATURATED AMMONIUM SULFATE, pH 7.0	Resolution 1.73 Å
4PAZ OXIDIZED MUTANT P80A PSEUDOAZURIN FROM A. FAECALIS Deposited 1997-02-20	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 24–146（123 aa）	Mutation：P80A	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；50MM SODIUM PHOSPHATE WITH 75% SATURATED AMMONIUM SULFATE, pH 7.0	Resolution 1.76 Å
4RH4 Zinc-substituted pseudoazurin solved by S/Zn-SAD phasing Deposited 2014-10-01	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 24–146（123 aa）	Not recorded	ZN ZINC ION × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.8；292 K；PROTEIN AT 15 MG/ML, 50MM NA-CITRATE, PH 5.8, 20 MM ZNCL2, 2.8 M AMMONIUM SULFATE, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 1.60 Å R-free 0.207
5PAZ REDUCED MUTANT P80A PSEUDOAZURIN FROM A. FAECALIS Deposited 1997-02-21	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 24–146（123 aa）	Mutation：P80A	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；50MM SODIUM PHOSPHATE WITH 75% SATURATED AMMONIUM SULFATE, pH 7.0	Resolution 1.76 Å
5X31 Pseudoazurin from Alcaligenes faecalis (space group P65) Deposited 2017-02-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 24–146（123 aa）	Not recorded	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2 M Sodium acetate trihydrate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 32.5-37.5% Polyethylene glycol 8000, 1.5 micro L of protein solution and 1.5 micro L reservoir	Resolution 2.60 Å R-free 0.239
5X31 Pseudoazurin from Alcaligenes faecalis (space group P65) Deposited 2017-02-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 24–146（123 aa）	Not recorded	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2 M Sodium acetate trihydrate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 32.5-37.5% Polyethylene glycol 8000, 1.5 micro L of protein solution and 1.5 micro L reservoir	Resolution 2.60 Å R-free 0.239
6PAZ OXIDIZED MUTANT P80I PSEUDOAZURIN FROM A. FAECALIS Deposited 1997-02-21	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 24–146（123 aa）	Mutation：P80I	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；50MM SODIUM PHOSPHATE WITH 75%, pH 7.0	Resolution 1.91 Å
7PAZ REDUCED MUTANT P80I PSEUDOAZURIN FROM A. FAECALIS Deposited 1997-02-21	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 24–146（123 aa）	Mutation：P80I	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；50MM SODIUM PHOSPHATE WITH 75%, pH 7.0	Resolution 2.00 Å
8K9N Subatomic resolution structure of Pseudoazurin from Alcaligenes faecalis Deposited 2023-08-01	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 24–146（123 aa）	Not recorded	CU COPPER (II) ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2.8 M ammonium sulfate	Resolution 0.86 Å R-free 0.163
8K9P Neutron X-ray joint structure of pseudoazurin from Alcaligenes faecalis Deposited 2023-08-01	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 24–146（123 aa）	Not recorded	CU COPPER (II) ION × 1 SO4 SULFATE ION × 1	Experimental method not declared X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2.8 M deuterated ammonium sulfate	Resolution not provided
8PAZ OXIDIZED NATIVE PSEUDOAZURIN FROM A. FAECALIS Deposited 1997-02-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 24–146（123 aa）	Not recorded	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；50MM SODIUM PHOSPHATE WITH 75% SATURATED AMMONIUM SULFATE., pH 6.5	Resolution 1.60 Å

16 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	AZUP_ALCFA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–123； UniProt 24–146

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3nyk
Deposition date deposition_date	2010-07-15
Structure title title	The structure of cobalt-substituted pseudoazurin from Alcaligenes faecalis
Keywords keywords	beta-sandwich, red-ox protein, divalent metal-ion, metalloprotein, METAL BINDING PROTEIN; METAL BINDING PROTEIN
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	14.66 Å
Radius of gyration Rg (electron density) rg_electron	13.15 Å
Forward intensity I(0) i0	3340750.00
Molecular weight molecular_weight	13120.0 kDa
Excluded volume excluded_volume	16593 Å³
Envelope volume envelope_volume	18194 Å³
Hydration-shell volume shell_volume	11658 Å³
Envelope diameter envelope_diameter	44.4 Å
Shell Rg shell_rg	19.10 Å
Envelope Rg envelope_rg	13.46 Å
Shape Rg shape_rg	13.13 Å
Total Rg total_rg	14.54 Å
Total atoms total_atoms	917
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	46.7 Å
Rg (real space) rg_real	14.54 Å
Rg uncertainty (real space) rg_real_error	0.35 Å
I(0) (real space) i0_real	3.3410e+06
I(0) uncertainty (real space) i0_real_error	4.2040e+04
Rg (reciprocal space) rg_reciprocal	14.55 Å
I(0) (reciprocal space) i0_reciprocal	3341000.0000
Solution quality estimate total_estimate	0.8821
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	17.7 Å
Skewness Skewness skewness	0.031
Kurtosis Kurtosis kurtosis	-0.489
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	706200.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.833; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.981

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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	Pseudoazurin
Molecular weight formula_weight	13383.5 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	1080

ENIEVHMLNKGAEGAMVFEPAYIKANPGDTVTFIPVDKGHNVESIKDMIPEGAEKFKSKINENYVLTVTQPGAYLVKCTPHYAMGMIALIAVGDSPANLDQIVSAKKPKIVQERLEKVIASAK

来源 Source

来源生物 organism	Alcaligenes faecalis
NCBI Class编号 ncbi_taxonomy_id	511
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	COBALT (II) ION
Molecular weight formula_weight	58.9 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	109

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3nyka_
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 (1 domains)

Domain ID domain_id	3nykA00
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	50.033 Å
Unit-cell length b length_b	50.033 Å
Unit-cell length c length_c	98.803 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	1.860 Å
Low-resolution limit resolution_low	43.330 Å
R factor r_factor	0.1509
R_work r_work	0.1496
R_free r_free	0.1781

fit	/app/data/saxs_computation/ny/3nyk/3nyk.fit
pddf	/app/data/pr_computation/ny/3nyk/3nyk.pr.out
profile	/app/data/saxs_computation/ny/3nyk/3nyk.dat

The structure of cobalt-substituted pseudoazurin from Alcaligenes faecalis

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

Pseudoazurin

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

Diffraction experiment Diffraction