SAXSdb — 1pza

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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	CU COPPER (II) ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.80 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 1PZA	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 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
1PZB THE CRYSTAL STRUCTURES OF REDUCED PSEUDOAZURIN FROM ALCALIGENES FAECALIS S-6 AT TWO PH VALUES Deposited 1994-08-03	Parsed fields agree	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
3NYK The structure of cobalt-substituted pseudoazurin from Alcaligenes faecalis Deposited 2010-07-15	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 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 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 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 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 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 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 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 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	1pza
Deposition date deposition_date	1994-09-06
Structure title title	THE CRYSTAL STRUCTURES OF REDUCED PSEUDOAZURIN FROM ALCALIGENES FAECALIS S-6 AT TWO PH VALUES
Keywords keywords	ELECTRON TRANSFER(CUPROPROTEIN); ELECTRON TRANSFER(CUPROPROTEIN)
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	13.11 Å
Forward intensity I(0) i0	3329510.00
Molecular weight molecular_weight	13125.0 kDa
Excluded volume excluded_volume	16591 Å³
Envelope volume envelope_volume	18042 Å³
Hydration-shell volume shell_volume	11617 Å³
Envelope diameter envelope_diameter	43.3 Å
Shell Rg shell_rg	19.04 Å
Envelope Rg envelope_rg	13.38 Å
Shape Rg shape_rg	13.08 Å
Total Rg total_rg	14.49 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	45.6 Å
Rg (real space) rg_real	14.46 Å
Rg uncertainty (real space) rg_real_error	0.24 Å
I(0) (real space) i0_real	3.3300e+06
I(0) uncertainty (real space) i0_real_error	3.6570e+04
Rg (reciprocal space) rg_reciprocal	14.47 Å
I(0) (reciprocal space) i0_reciprocal	3330000.0000
Solution quality estimate total_estimate	0.8919
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	45.0 Å
Skewness Skewness skewness	0.025
Kurtosis Kurtosis kurtosis	-0.498
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	732700.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.868; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; 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	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	1015

ENIEVHMLNKGAEGAMVFEPAYIKANPGDTVTFIPVDKGHNVESIKDMIPEGAEKFKSKINENYVLTVTQPGAYLVKCTPHYAMGMIALIAVGDSPANLDQIVSAKKPKIVQERLEKVIASAK

来源 Source

来源生物 organism	Alcaligenes faecalis
NCBI Class编号 ncbi_taxonomy_id	511

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	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	97

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1pzaa_
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	1pzaA00
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 (2)

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Unit-cell length a length_a	49.900 Å
Unit-cell length b length_b	49.900 Å
Unit-cell length c length_c	99.100 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	1.800 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1780
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/pz/1pza/1pza.fit
pddf	/app/data/pr_computation/pz/1pza/1pza.pr.out
profile	/app/data/saxs_computation/pz/1pza/1pza.dat

THE CRYSTAL STRUCTURES OF REDUCED PSEUDOAZURIN FROM ALCALIGENES FAECALIS S-6 AT TWO PH VALUES

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