5d4j

Chloride-bound form of a copper nitrite reductase from Alcaligenes faecals

Method: X-RAY DIFFRACTION Dmax: 85.2 Å Quality: EXCELLENT

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

Copper-containing nitrite reductase

Alcaligenes faecalis

UniProt P38501

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 homooligomer Homooligomer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 40–376 Chain B; UniProt 40–376 Chain C; UniProt 40–376 Fragment:UNP residues 40-376 CU COPPER (II) ION × 6 CL CHLORIDE ION × 3 GOL GLYCEROL × 10 ACY ACETIC ACID × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 4.1;293 K;1:1 mixture of the purified protein solution (40 mg/ml) and a reservoir solution composed of 100 mM sodium acetate (pH 4.1) and 7% PEG 4000 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.

46 other PDB entries and 46 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NIR_ALCFA
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–338; UniProt 40–376 Author chain B; PDBConstruct 2–338; UniProt 40–376 Author chain C; PDBConstruct 2–338; UniProt 40–376

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 5d4j

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5d4j
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5d4j
Deposition date deposition_date2015-08-07
Structure title titleChloride-bound form of a copper nitrite reductase from Alcaligenes faecals
Keywords keywordscopper, oxidoreductase; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier28.61
Radius of gyration Rg (electron density) rg_electron27.59
Forward intensity I(0) i0189840000.00
Molecular weight molecular_weight110270.0 kDa
Excluded volume excluded_volume137990 ų
Envelope volume envelope_volume158190 ų
Hydration-shell volume shell_volume44886 ų
Envelope diameter envelope_diameter88.6
Shell Rg shell_rg37.11
Envelope Rg envelope_rg27.89
Shape Rg shape_rg27.56
Total Rg total_rg28.53
Total atoms total_atoms7756
Residues n_residues1007
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 dmax85.2
Rg (real space) rg_real28.43
Rg uncertainty (real space) rg_real_error0.37
I(0) (real space) i0_real1.8980e+08
I(0) uncertainty (real space) i0_real_error2.4920e+06
Rg (reciprocal space) rg_reciprocal28.51
I(0) (reciprocal space) i0_reciprocal189900000.0000
Solution quality estimate total_estimate0.9082
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary37.2
Skewness Skewness skewness0.103
Kurtosis Kurtosis kurtosis-0.566
Angular range angular_range— – 0.2750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha66940000.0000
Real-space data points n_real_points56
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.954; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.959

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd5d4ja1
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
Domain ID domain_idd5d4ja2
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
Domain ID domain_idd5d4jb1
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
Domain ID domain_idd5d4jb2
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
Domain ID domain_idd5d4jc1
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
Domain ID domain_idd5d4jc2
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 (6 domains)

Domain ID domain_id5d4jA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id5d4jA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id5d4jB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id5d4jB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id5d4jC01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id5d4jC02
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)