3zoy

Crystal Structure of N64Del Mutant of Nitrosomonas europaea Cytochrome c552 (hexagonal space group)

Method: X-RAY DIFFRACTION Dmax: 81.5 Å Quality: GOOD

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

CYTOCHROME C-552

NITROSOMONAS EUROPAEA

UniProt P95339

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 monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 23–103 Mutation:YES HEC HEME C × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 8.5;0.1 M TRIS-HCL PH 8.5, 3.1 M AMMONIUM SULFATE Resolution 2.30 Å R-free 0.226
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 23–103 Mutation:YES HEC HEME C × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 8.5;0.1 M TRIS-HCL PH 8.5, 3.1 M AMMONIUM SULFATE Resolution 2.30 Å R-free 0.226
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 23–103 Mutation:YES HEC HEME C × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 8.5;0.1 M TRIS-HCL PH 8.5, 3.1 M AMMONIUM SULFATE Resolution 2.30 Å R-free 0.226
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain D; UniProt 23–103 Mutation:YES HEC HEME C × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 8.5;0.1 M TRIS-HCL PH 8.5, 3.1 M AMMONIUM SULFATE Resolution 2.30 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.

5 other PDB entries and 25 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CY552_NITEU
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–80; UniProt 23–103 Author chain B; PDBConstruct 1–80; UniProt 23–103 Author chain C; PDBConstruct 1–80; UniProt 23–103 Author chain D; PDBConstruct 1–80; UniProt 23–103

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 3zoy

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id3zoy
Deposition date deposition_date2013-02-26
Structure title titleCrystal Structure of N64Del Mutant of Nitrosomonas europaea Cytochrome c552 (hexagonal space group)
Keywords keywordsHEMEPROTEIN, ELECTRON TRANSPORT; ELECTRON TRANSPORT
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier22.40
Radius of gyration Rg (electron density) rg_electron21.66
Forward intensity I(0) i020606300.00
Molecular weight molecular_weight35614.0 kDa
Excluded volume excluded_volume45010 ų
Envelope volume envelope_volume52472 ų
Hydration-shell volume shell_volume20973 ų
Envelope diameter envelope_diameter81.9
Shell Rg shell_rg27.82
Envelope Rg envelope_rg21.80
Shape Rg shape_rg21.61
Total Rg total_rg22.63
Total atoms total_atoms2498
Residues n_residues318
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 dmax81.5
Rg (real space) rg_real22.42
Rg uncertainty (real space) rg_real_error0.71
I(0) (real space) i0_real2.0610e+07
I(0) uncertainty (real space) i0_real_error2.8680e+05
Rg (reciprocal space) rg_reciprocal22.42
I(0) (reciprocal space) i0_reciprocal20610000.0000
Solution quality estimate total_estimate0.8432
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.2
Skewness Skewness skewness0.386
Kurtosis Kurtosis kurtosis-0.202
Angular range angular_range— – 0.3550 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha10360000.0000
Real-space data points n_real_points67
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.691; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.890; Smooth: 0.995

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd3zoya_
Class classa — All alpha proteins
Fold Fold folda.3 — Cytochrome c
Superfamily Superfamily superfamilya.3.1 — Cytochrome c
Family Family familya.3.1.0 — automated matches
Domain ID domain_idd3zoyb_
Class classa — All alpha proteins
Fold Fold folda.3 — Cytochrome c
Superfamily Superfamily superfamilya.3.1 — Cytochrome c
Family Family familya.3.1.0 — automated matches
Domain ID domain_idd3zoyc_
Class classa — All alpha proteins
Fold Fold folda.3 — Cytochrome c
Superfamily Superfamily superfamilya.3.1 — Cytochrome c
Family Family familya.3.1.0 — automated matches
Domain ID domain_idd3zoyd_
Class classa — All alpha proteins
Fold Fold folda.3 — Cytochrome c
Superfamily Superfamily superfamilya.3.1 — Cytochrome c
Family Family familya.3.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id3zoyA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain
Domain ID domain_id3zoyB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain
Domain ID domain_id3zoyC00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain
Domain ID domain_id3zoyD00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain

8. Citations (1)

9. Files and Curves (10)