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1cot

X-RAY STRUCTURE OF THE CYTOCHROME C2 ISOLATED FROM PARACOCCUS DENITRIFICANS REFINED TO 1.7 ANGSTROMS RESOLUTION

Method: X-RAY DIFFRACTION Dmax: 50.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

CYTOCHROME C2

Paracoccus denitrificans

UniProt P00096

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 21–149 Not recorded HEC HEME C × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 1.70 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.

Other PDB Difference from Current Entry 1COT Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
155C THE STRUCTURE OF PARACOCCUS DENITRIFICANS CYTOCHROME C550 Deposited 1976-08-01 Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 23–142（120 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) HEM PROTOPORPHYRIN IX CONTAINING FE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CY550_PARDE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–129； UniProt 21–149

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 1cot

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1cot
Deposition date deposition_date1994-07-06
Structure title titleX-RAY STRUCTURE OF THE CYTOCHROME C2 ISOLATED FROM PARACOCCUS DENITRIFICANS REFINED TO 1.7 ANGSTROMS RESOLUTION
Keywords keywordsELECTRON TRANSPORT; ELECTRON TRANSPORT
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier14.84 Å
Radius of gyration Rg (electron density) rg_electron13.51 Å
Forward intensity I(0) i03660870.00
Molecular weight molecular_weight13679.0 kDa
Excluded volume excluded_volume17154 ų
Envelope volume envelope_volume18595 ų
Hydration-shell volume shell_volume11694 ų
Envelope diameter envelope_diameter49.5 Å
Shell Rg shell_rg19.38 Å
Envelope Rg envelope_rg13.96 Å
Shape Rg shape_rg13.47 Å
Total Rg total_rg14.83 Å
Total atoms total_atoms959
Residues n_residues121
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax50.0 Å
Rg (real space) rg_real14.76 Å
Rg uncertainty (real space) rg_real_error0.27 Å
I(0) (real space) i0_real3.6610e+06
I(0) uncertainty (real space) i0_real_error4.1410e+04
Rg (reciprocal space) rg_reciprocal14.77 Å
I(0) (reciprocal space) i0_reciprocal3661000.0000
Solution quality estimate total_estimate0.8697
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary48.7 Å
Skewness Skewness skewness0.183
Kurtosis Kurtosis kurtosis-0.319
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha613600.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.768; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.999
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1cota_
Class classa — All alpha proteins
Fold Fold folda.3 — Cytochrome c
Superfamily Superfamily superfamilya.3.1 — Cytochrome c
Family Family familya.3.1.1 — monodomain cytochrome c

CATH v4.4 (1 domains)

Domain ID domain_id1cotA00
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
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8. Citations (1)

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9. Files and Curves (10)