SAXSdb — 1py0

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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	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

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 1PY0	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 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）	Not recorded	CU COPPER (II) ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.55 Å
1PZA THE CRYSTAL STRUCTURES OF REDUCED PSEUDOAZURIN FROM ALCALIGENES FAECALIS S-6 AT TWO PH VALUES Deposited 1994-09-06	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 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 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）	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 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）	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 mutation/modification 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
3NYK The structure of cobalt-substituted pseudoazurin from Alcaligenes faecalis Deposited 2010-07-15	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）	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
3PAZ REDUCED NATIVE 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）	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 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）	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 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）	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 mutation/modification 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 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）	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 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 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 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）	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 3–125； 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	1py0
Deposition date deposition_date	2003-07-07
Structure title title	Crystal structure of E51C/E54C Psaz from A.faecalis with CLaNP probe
Keywords keywords	cupredoxin, NMR probe, 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	15.17 Å
Radius of gyration Rg (electron density) rg_electron	13.64 Å
Forward intensity I(0) i0	3956060.00
Molecular weight molecular_weight	13931.0 kDa
Excluded volume excluded_volume	17400 Å³
Envelope volume envelope_volume	19377 Å³
Hydration-shell volume shell_volume	12051 Å³
Envelope diameter envelope_diameter	49.4 Å
Shell Rg shell_rg	19.50 Å
Envelope Rg envelope_rg	13.98 Å
Shape Rg shape_rg	13.55 Å
Total Rg total_rg	15.14 Å
Total atoms total_atoms	961
Residues n_residues	121
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	51.1 Å
Rg (real space) rg_real	15.05 Å
Rg uncertainty (real space) rg_real_error	0.30 Å
I(0) (real space) i0_real	3.9560e+06
I(0) uncertainty (real space) i0_real_error	4.2090e+04
Rg (reciprocal space) rg_reciprocal	15.06 Å
I(0) (reciprocal space) i0_reciprocal	3956000.0000
Solution quality estimate total_estimate	0.7894
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.3 Å
Skewness Skewness skewness	0.050
Kurtosis Kurtosis kurtosis	-0.440
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	714000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.753; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Pseudoazurin
Molecular weight formula_weight	13489.7 kDa
Mutation mutation	E51C, E54C
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	1032

ASENIEVHMLNKGAEGAMVFEPAYIKANPGDTVTFIPVDKGHNVESIKDMIPCGACKFKSKINENYVLTVTQPGAYLVKCTPHYAMGMIALIAVGDSPANLDQIVSAKKPKIVQERLEKVIASAK

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 BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	YTTRIUM ION
Molecular weight formula_weight	88.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	7,10,13-TRI(CARBOXYMETHYL)-5,15-DIOXO-4,7,10,13,16-PENTAAZA-1,19-DITHIANONADECANE
Molecular weight formula_weight	511.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	71

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1py0a1
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	d1py0a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	1py0A00
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	42.700 Å
Unit-cell length b length_b	42.700 Å
Unit-cell length c length_c	116.900 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	2.000 Å
Low-resolution limit resolution_low	37.010 Å
R factor r_factor	0.1961
R_work r_work	0.1930
R_free r_free	0.2318

fit	/app/data/saxs_computation/py/1py0/1py0.fit
pddf	/app/data/pr_computation/py/1py0/1py0.pr.out
profile	/app/data/saxs_computation/py/1py0/1py0.dat

Crystal structure of E51C/E54C Psaz from A.faecalis with CLaNP probe