4yse

High resolution synchrotron structure of copper nitrite reductase from Alcaligenes faecalis

Method: X-RAY DIFFRACTION Dmax: 85.4 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 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 6 ACY ACETIC ACID × 5 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 4;293 K;100mM sodium acetate, pH 4, 8% PEG4000 Resolution 1.20 Å R-free 0.168

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 4yse

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4yse
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4yse
Deposition date deposition_date2015-03-17
Structure title titleHigh resolution synchrotron structure of copper nitrite reductase from Alcaligenes faecalis
Keywords keywordsNitrite, Copper, Reductase, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier28.70
Radius of gyration Rg (electron density) rg_electron27.69
Forward intensity I(0) i0188147000.00
Molecular weight molecular_weight110440.0 kDa
Excluded volume excluded_volume138480 ų
Envelope volume envelope_volume158590 ų
Hydration-shell volume shell_volume44930 ų
Envelope diameter envelope_diameter88.5
Shell Rg shell_rg37.20
Envelope Rg envelope_rg27.95
Shape Rg shape_rg27.65
Total Rg total_rg28.65
Total atoms total_atoms7775
Residues n_residues1011
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 dmax85.4
Rg (real space) rg_real28.52
Rg uncertainty (real space) rg_real_error0.44
I(0) (real space) i0_real1.8810e+08
I(0) uncertainty (real space) i0_real_error2.5880e+06
Rg (reciprocal space) rg_reciprocal28.60
I(0) (reciprocal space) i0_reciprocal188200000.0000
Solution quality estimate total_estimate0.9086
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary35.7
Skewness Skewness skewness0.106
Kurtosis Kurtosis kurtosis-0.565
Angular range angular_range— – 0.2750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha66070000.0000
Real-space data points n_real_points56
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.955; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.964

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd4ysea1
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_idd4ysea2
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_idd4yseb1
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_idd4yseb2
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_idd4ysec1
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_idd4ysec2
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_id4yseA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id4yseA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id4yseB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id4yseB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id4yseC01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id4yseC02
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)