2ppf

Reduced mutant D98N of AfNiR exposed to nitric oxide

Method: X-RAY DIFFRACTION Dmax: 84.4 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 Mutation:D98N CU1 COPPER (I) ION × 5 CU COPPER (II) ION × 3 ACT ACETATE ION × 8 NO NITRIC OXIDE × 4 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4;298 K;7-12% polyethylene glycol 4000, 75 mM acetamide and 10 mM sodium acetate buffer, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 1.65 Å R-free 0.170

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 1–337; UniProt 40–376 Author chain B; PDBConstruct 1–337; UniProt 40–376 Author chain C; PDBConstruct 1–337; 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 2ppf

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2ppf
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id2ppf
Deposition date deposition_date2007-04-28
Structure title titleReduced mutant D98N of AfNiR exposed to nitric oxide
Keywords keywordsnitrite reductase, D98N, nitric oxide, denitrification, bacteria, Oxidoreductase; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier28.65
Radius of gyration Rg (electron density) rg_electron27.63
Forward intensity I(0) i0190528000.00
Molecular weight molecular_weight110040.0 kDa
Excluded volume excluded_volume137520 ų
Envelope volume envelope_volume158510 ų
Hydration-shell volume shell_volume44924 ų
Envelope diameter envelope_diameter88.6
Shell Rg shell_rg37.13
Envelope Rg envelope_rg27.94
Shape Rg shape_rg27.60
Total Rg total_rg28.58
Total atoms total_atoms7741
Residues n_residues1009
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 dmax84.4
Rg (real space) rg_real28.48
Rg uncertainty (real space) rg_real_error0.40
I(0) (real space) i0_real1.9050e+08
I(0) uncertainty (real space) i0_real_error2.6790e+06
Rg (reciprocal space) rg_reciprocal28.55
I(0) (reciprocal space) i0_reciprocal190500000.0000
Solution quality estimate total_estimate0.9089
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary36.8
Skewness Skewness skewness0.104
Kurtosis Kurtosis kurtosis-0.567
Angular range angular_range— – 0.2750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha63970000.0000
Real-space data points n_real_points56
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.963; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.943

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd2ppfa1
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_idd2ppfa2
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_idd2ppfb1
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_idd2ppfb2
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_idd2ppfc1
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_idd2ppfc2
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_id2ppfA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id2ppfA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id2ppfB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id2ppfB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id2ppfC01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id2ppfC02
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)