5b1j

Crystal structure of the electron-transfer complex of copper nitrite reductase with a cupredoxin

Method: X-RAY DIFFRACTION Dmax: 105.1 Å Quality: GOOD

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

Copper-containing nitrite reductase

OrganismNot specified

UniProt O68601

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 25–360 Chain B; UniProt 25–360 Fragment:UNP residues 25-360 Blue copper protein × 1 (A7VL37) 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

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.

36 other PDB entries and 48 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name O68601_ALCXX
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–336; UniProt 25–360 Author chain B; PDBConstruct 1–336; UniProt 25–360

Blue copper protein

OrganismNot specified

UniProt A7VL37

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain C; UniProt 27–150 Not recorded Copper-containing nitrite reductase × 2 (O68601) 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

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.

1 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A7VL37_9RHIZ
Isoform
PDB entities 2
Chains and sequence ranges 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.

SAXS scattering curve SAXS Profile

SAXS profile for 5b1j

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5b1j
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5b1j
Deposition date deposition_date2015-12-04
Structure title titleCrystal structure of the electron-transfer complex of copper nitrite reductase with a cupredoxin
Keywords keywordscomplex, copper nitrite reductase, electron transfer, OXIDOREDUCTASE-ELECTRON TRANSPORT complex; OXIDOREDUCTASE/ELECTRON TRANSPORT
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier30.23
Radius of gyration Rg (electron density) rg_electron29.69
Forward intensity I(0) i0117979000.00
Molecular weight molecular_weight86110.0 kDa
Excluded volume excluded_volume107800 ų
Envelope volume envelope_volume138510 ų
Hydration-shell volume shell_volume38762 ų
Envelope diameter envelope_diameter110.7
Shell Rg shell_rg36.79
Envelope Rg envelope_rg30.01
Shape Rg shape_rg29.70
Total Rg total_rg30.31
Total atoms total_atoms6055
Residues n_residues792
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax105.1
Rg (real space) rg_real30.16
Rg uncertainty (real space) rg_real_error0.85
I(0) (real space) i0_real1.1800e+08
I(0) uncertainty (real space) i0_real_error1.8390e+06
Rg (reciprocal space) rg_reciprocal30.19
I(0) (reciprocal space) i0_reciprocal118000000.0000
Solution quality estimate total_estimate0.8770
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary36.4
Skewness Skewness skewness0.246
Kurtosis Kurtosis kurtosis-0.442
Angular range angular_range— – 0.2600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha27710000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.815; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.978

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_idd5b1ja1
Class classb — All beta proteins
Fold Fold foldb.6 — Cupredoxin-like
Superfamily Superfamily superfamilyb.6.1 — Cupredoxins
Family Family familyb.6.1.3 — Multidomain cupredoxins
Domain ID domain_idd5b1ja2
Class classb — All beta proteins
Fold Fold foldb.6 — Cupredoxin-like
Superfamily Superfamily superfamilyb.6.1 — Cupredoxins
Family Family familyb.6.1.3 — Multidomain cupredoxins
Domain ID domain_idd5b1jb1
Class classb — All beta proteins
Fold Fold foldb.6 — Cupredoxin-like
Superfamily Superfamily superfamilyb.6.1 — Cupredoxins
Family Family familyb.6.1.3 — Multidomain cupredoxins
Domain ID domain_idd5b1jb2
Class classb — All beta proteins
Fold Fold foldb.6 — Cupredoxin-like
Superfamily Superfamily superfamilyb.6.1 — Cupredoxins
Family Family familyb.6.1.3 — Multidomain cupredoxins
Domain ID domain_idd5b1jc_
Class classb — All beta proteins
Fold Fold foldb.6 — Cupredoxin-like
Superfamily Superfamily superfamilyb.6.1 — Cupredoxins
Family Family familyb.6.1.0 — automated matches

CATH v4.4 (5 domains)

Domain ID domain_id5b1jA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id5b1jA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id5b1jB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id5b1jB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id5b1jC00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins

8. Citations (1)

9. Files and Curves (10)