SAXSdb — 3ef4

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

Blue copper protein

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 27–150	Not recorded	CU COPPER (II) ION × 1 PO4 PHOSPHATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4；277 K；3.2M Ammonium Phosphate, 0.05M Potassium Phosphate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.18 Å R-free 0.169
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 27–150	Not recorded	CU COPPER (II) ION × 1 PO4 PHOSPHATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4；277 K；3.2M Ammonium Phosphate, 0.05M Potassium Phosphate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.18 Å R-free 0.169
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 27–150	Not recorded	CU COPPER (II) ION × 1 PO4 PHOSPHATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4；277 K；3.2M Ammonium Phosphate, 0.05M Potassium Phosphate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.18 Å R-free 0.169

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 3EF4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5B1J Crystal structure of the electron-transfer complex of copper nitrite reductase with a cupredoxin Deposited 2015-12-04	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 27–150（124 aa）	Not recorded	CU COPPER (II) ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG 3350, potassium chloride	Resolution 3.00 Å R-free 0.233

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A7VL37_9RHIZ
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–124； UniProt 27–150 Author chain B； PDBConstruct 1–124； UniProt 27–150 Author chain C； PDBConstruct 1–124； UniProt 27–150

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	3ef4
Deposition date deposition_date	2008-09-08
Structure title title	Crystal structure of native pseudoazurin from Hyphomicrobium denitrificans
Keywords keywords	copper, electron transfer, blue copper protein, 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	24.80 Å
Radius of gyration Rg (electron density) rg_electron	24.09 Å
Forward intensity I(0) i0	32452400.00
Molecular weight molecular_weight	41588.0 kDa
Excluded volume excluded_volume	51031 Å³
Envelope volume envelope_volume	62109 Å³
Hydration-shell volume shell_volume	22237 Å³
Envelope diameter envelope_diameter	80.3 Å
Shell Rg shell_rg	30.23 Å
Envelope Rg envelope_rg	24.16 Å
Shape Rg shape_rg	24.10 Å
Total Rg total_rg	24.79 Å
Total atoms total_atoms	2892
Residues n_residues	372
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	75.8 Å
Rg (real space) rg_real	24.80 Å
Rg uncertainty (real space) rg_real_error	0.47 Å
I(0) (real space) i0_real	3.2450e+07
I(0) uncertainty (real space) i0_real_error	3.9490e+05
Rg (reciprocal space) rg_reciprocal	24.80 Å
I(0) (reciprocal space) i0_reciprocal	32450000.0000
Solution quality estimate total_estimate	0.9076
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.1 Å
Skewness Skewness skewness	0.251
Kurtosis Kurtosis kurtosis	-0.678
Angular range angular_range	— – 0.3200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5540000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.960; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.961; Smooth: 0.954

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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	Blue copper protein
Molecular weight formula_weight	13590.7 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	3481

AEHIVEMRNKDDAGNTMVFQPGFVKVEAGDTVKFVPTDKSHNAESVREVWPEGVAPVKGGFSKEVVFNAEKEGLYVLKCAPHYGMGMVVLVQVGKPVNLDQIKEYKATGLAKKRLDGEIAKVVQ

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	3

Entity 3 Entity 3 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	15

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	500

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d3ef4a_
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.0 — automated matches

Domain ID domain_id	d3ef4b_
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.0 — automated matches

Domain ID domain_id	d3ef4c_
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.0 — automated matches

CATH v4.4 (3 domains)

Domain ID domain_id	3ef4A00
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	3ef4B00
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	3ef4C00
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	97.690 Å
Unit-cell length b length_b	50.623 Å
Unit-cell length c length_c	82.378 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.98 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.180 Å
Low-resolution limit resolution_low	44.950 Å
R factor r_factor	0.1350
R_work r_work	0.1350
R_free r_free	0.1690

fit	/app/data/saxs_computation/ef/3ef4/3ef4.fit
pddf	/app/data/pr_computation/ef/3ef4/3ef4.pr.out
profile	/app/data/saxs_computation/ef/3ef4/3ef4.dat

Crystal structure of native pseudoazurin from Hyphomicrobium denitrificans

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

Blue copper protein

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