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1cxa

CRYSTALLIZATION AND X-RAY STRUCTURE DETERMINATION OF CYTOCHROME C2 FROM RHODOBACTER SPHAEROIDES IN THREE CRYSTAL FORMS

Method: X-RAY DIFFRACTION Dmax: 45.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

CYTOCHROME C2

Rhodobacter sphaeroides

UniProt P00095

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 22–145 Not recorded IMD IMIDAZOLE × 1 HEC HEME C × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.20 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 1CXA Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1CXC CRYSTALLIZATION AND X-RAY STRUCTURE DETERMINATION OF CYTOCHROME C2 FROM RHODOBACTER SPHAEROIDES IN THREE CRYSTAL FORMS Deposited 1994-02-14 Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–145（124 aa）
Not recorded HEC HEME C × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.60 Å
1L9B X-Ray Structure of the Cytochrome-c(2)-Photosynthetic Reaction Center Electron Transfer Complex from Rhodobacter sphaeroides in Type II Co-Crystals Deposited 2002-03-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 22–145（124 aa）
Not recorded NA SODIUM ION × 1 BCL BACTERIOCHLOROPHYLL A × 4 BPH BACTERIOPHEOPHYTIN A × 2 LDA LAURYL DIMETHYLAMINE-N-OXIDE × 9 HTO HEPTANE-1,2,3-TRIOL × 2 FE2 FE (II) ION × 1 CL CHLORIDE ION × 1 U10 UBIQUINONE-10 × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；292 K；10% PEG 4000, 0.06%(w/v) lauryldimethylamine-N-oxide, 3.9%(w/v) heptane-1,2,3-triol, 15 mM Tricine, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 2.40 Å R-free 0.264
1L9J X-Ray Structure of the Cytochrome-c(2)-Photosynthetic Reaction Center Electron Transfer Complex from Rhodobacter sphaeroides in Type I Co-Crystals Deposited 2002-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 22–145（124 aa）
Not recorded BCL BACTERIOCHLOROPHYLL A × 4 BPH BACTERIOPHEOPHYTIN A × 2 FE2 FE (II) ION × 1 CL CHLORIDE ION × 1 U10 UBIQUINONE-10 × 1 LDA LAURYL DIMETHYLAMINE-N-OXIDE × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；292 K；PEG 4000, lauryl-dimethylamine-N-oxide, heptane-1,2,3-triol, tricine buffer, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 3.25 Å R-free 0.287
1L9J X-Ray Structure of the Cytochrome-c(2)-Photosynthetic Reaction Center Electron Transfer Complex from Rhodobacter sphaeroides in Type I Co-Crystals Deposited 2002-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 22–145（124 aa）
Not recorded BCL BACTERIOCHLOROPHYLL A × 4 BPH BACTERIOPHEOPHYTIN A × 2 FE2 FE (II) ION × 1 CL CHLORIDE ION × 1 U10 UBIQUINONE-10 × 1 LDA LAURYL DIMETHYLAMINE-N-OXIDE × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；292 K；PEG 4000, lauryl-dimethylamine-N-oxide, heptane-1,2,3-triol, tricine buffer, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 3.25 Å R-free 0.287
2CXB CRYSTALLIZATION AND X-RAY STRUCTURE DETERMINATION OF CYTOCHROME C2 FROM RHODOBACTER SPHAEROIDES IN THREE CRYSTAL FORMS Deposited 1994-04-21 Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–145（124 aa）
Not recorded HEC HEME C × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.95 Å
2CXB CRYSTALLIZATION AND X-RAY STRUCTURE DETERMINATION OF CYTOCHROME C2 FROM RHODOBACTER SPHAEROIDES IN THREE CRYSTAL FORMS Deposited 1994-04-21 Different ligand/ion Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 22–145（124 aa）
Not recorded HEC HEME C × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.95 Å

4 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CYC2_RHOSH
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–124； UniProt 22–145

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 1cxa

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1cxa
Deposition date deposition_date1994-02-14
Structure title titleCRYSTALLIZATION AND X-RAY STRUCTURE DETERMINATION OF CYTOCHROME C2 FROM RHODOBACTER SPHAEROIDES IN THREE CRYSTAL FORMS
Keywords keywordsELECTRON TRANSPORT (CYTOCHROME); ELECTRON TRANSPORT (CYTOCHROME)
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_guinier14.55 Å
Radius of gyration Rg (electron density) rg_electron13.26 Å
Forward intensity I(0) i03648110.00
Molecular weight molecular_weight13484.0 kDa
Excluded volume excluded_volume16792 ų
Envelope volume envelope_volume18137 ų
Hydration-shell volume shell_volume11592 ų
Envelope diameter envelope_diameter45.2 Å
Shell Rg shell_rg19.10 Å
Envelope Rg envelope_rg13.63 Å
Shape Rg shape_rg13.24 Å
Total Rg total_rg14.54 Å
Total atoms total_atoms954
Residues n_residues124
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 dmax45.8 Å
Rg (real space) rg_real14.45 Å
Rg uncertainty (real space) rg_real_error0.24 Å
I(0) (real space) i0_real3.6480e+06
I(0) uncertainty (real space) i0_real_error4.0270e+04
Rg (reciprocal space) rg_reciprocal14.46 Å
I(0) (reciprocal space) i0_reciprocal3648000.0000
Solution quality estimate total_estimate0.8930
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary18.6 Å
Skewness Skewness skewness0.128
Kurtosis Kurtosis kurtosis-0.355
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha628000.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.874; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.989
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1cxaa_
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_id1cxaA00
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)