1as8

STRUCTURE OF NITRITE BOUND TO REDUCED ALCALIGENES FAECALIS NITRITE REDUCTASE AT CRYO TEMPERATURE

Method: X-RAY DIFFRACTION Dmax: 81.4 Å Quality: EXCELLENT

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

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 34–376 Chain B; UniProt 34–376 Chain C; UniProt 34–376 Not recorded CU COPPER (II) ION × 6 NO2 NITRITE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:pH 4.5;10% PEG4000, 0.1 SODIUM ACETATE PH 4.5 Resolution 1.85 Å

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 1–343; UniProt 34–376 Author chain B; PDBConstruct 1–343; UniProt 34–376 Author chain C; PDBConstruct 1–343; UniProt 34–376

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 1as8

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1as8
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1as8
Deposition date deposition_date1997-08-13
Structure title titleSTRUCTURE OF NITRITE BOUND TO REDUCED ALCALIGENES FAECALIS NITRITE REDUCTASE AT CRYO TEMPERATURE
Keywords keywordsOXIDOREDUCTASE, NITRITE, COPPER, DENITRIFICATION; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier28.58
Radius of gyration Rg (electron density) rg_electron27.58
Forward intensity I(0) i0186557000.00
Molecular weight molecular_weight109270.0 kDa
Excluded volume excluded_volume136680 ų
Envelope volume envelope_volume156370 ų
Hydration-shell volume shell_volume44534 ų
Envelope diameter envelope_diameter87.9
Shell Rg shell_rg37.02
Envelope Rg envelope_rg27.81
Shape Rg shape_rg27.55
Total Rg total_rg28.52
Total atoms total_atoms9243
Residues n_residues1008
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 dmax81.4
Rg (real space) rg_real28.40
Rg uncertainty (real space) rg_real_error0.29
I(0) (real space) i0_real1.8660e+08
I(0) uncertainty (real space) i0_real_error2.1480e+06
Rg (reciprocal space) rg_reciprocal28.48
I(0) (reciprocal space) i0_reciprocal186600000.0000
Solution quality estimate total_estimate0.9032
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary37.0
Skewness Skewness skewness0.100
Kurtosis Kurtosis kurtosis-0.570
Angular range angular_range— – 0.2750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha61330000.0000
Real-space data points n_real_points56
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.983; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.809

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd1as8a1
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_idd1as8a2
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_idd1as8b1
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_idd1as8b2
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_idd1as8c1
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_idd1as8c2
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

CATH v4.4 (6 domains)

Domain ID domain_id1as8A01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id1as8A02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id1as8B01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id1as8B02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id1as8C01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id1as8C02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins

8. Citations (3)

9. Files and Curves (10)