3h4h

Met94Thr/Phe312Cys variant of nitrite reductase from Alcaligenes faecalis

Method: X-RAY DIFFRACTION Dmax: 83.5 Å Quality: GOOD

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 41–375 Chain B; UniProt 41–375 Chain C; UniProt 41–375 Non-standard monomer:Yes (specific site not provided by mmCIF) CU COPPER (II) ION × 6 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.5;298 K;pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 1.60 Å R-free 0.226

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 1–335; UniProt 41–375 Author chain B; PDBConstruct 1–335; UniProt 41–375 Author chain C; PDBConstruct 1–335; UniProt 41–375

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 3h4h

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3h4h
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3h4h
Deposition date deposition_date2009-04-20
Structure title titleMet94Thr/Phe312Cys variant of nitrite reductase from Alcaligenes faecalis
Keywords keywords;nitrite reductase, high-throuhput screening, oxidase, copper, FAD, Flavoprotein, Metal-binding, Nitrate assimilation, Oxidoreductase, Periplasm, Pyrrolidone carboxylic acid ;; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier28.53
Radius of gyration Rg (electron density) rg_electron27.54
Forward intensity I(0) i0186179000.00
Molecular weight molecular_weight108790.0 kDa
Excluded volume excluded_volume136020 ų
Envelope volume envelope_volume156200 ų
Hydration-shell volume shell_volume44490 ų
Envelope diameter envelope_diameter88.2
Shell Rg shell_rg36.97
Envelope Rg envelope_rg27.81
Shape Rg shape_rg27.51
Total Rg total_rg28.46
Total atoms total_atoms7659
Residues n_residues1002
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 dmax83.5
Rg (real space) rg_real28.36
Rg uncertainty (real space) rg_real_error0.45
I(0) (real space) i0_real1.8620e+08
I(0) uncertainty (real space) i0_real_error2.5480e+06
Rg (reciprocal space) rg_reciprocal28.44
I(0) (reciprocal space) i0_reciprocal186200000.0000
Solution quality estimate total_estimate0.8362
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary35.8
Skewness Skewness skewness0.103
Kurtosis Kurtosis kurtosis-0.566
Angular range angular_range— – 0.2800 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha66110000.0000
Real-space data points n_real_points57
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.965; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd3h4ha1
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_idd3h4ha2
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_idd3h4hb1
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_idd3h4hb2
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_idd3h4hc1
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_idd3h4hc2
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_id3h4hA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id3h4hA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id3h4hB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id3h4hB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id3h4hC01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id3h4hC02
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)