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2bpn

SOLUTION STRUCTURE OF DESULFOVIBRIO VULGARIS (HILDENBOROUGH) FERRICYTOCHROME C3, NMR, 20 STRUCTURES

Method: SOLUTION NMR Dmax: 41.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

CYTOCHROME C3

OrganismNot specified

UniProt P00131

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 23–129 Fragment：CYTOCHROME C3, RESIDUES 23-129 HEC HEME C × 4 SOLUTION NMR NMR measurement conditions：pH 7.1；303 K NMR sample composition：92% WATER/8% D2O AND 100% D2O Resolution not provided

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 2BPN Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1A2I SOLUTION STRUCTURE OF DESULFOVIBRIO VULGARIS (HILDENBOROUGH) FERROCYTOCHROME C3, NMR, 20 STRUCTURES Deposited 1998-01-05 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 23–129（107 aa）
Not recorded HEC HEME C × 4 SOLUTION NMR
NMR measurement conditions pH 8.5；303 K
Resolution not provided
1GX7 Best model of the electron transfer complex between cytochrome c3 and [Fe]-hydrogenase Deposited 2002-03-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 23–129（107 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 3 PDT 1,3-PROPANEDITHIOL × 1 FE2 FE (II) ION × 2 CYN CYANIDE ION × 2 CMO CARBON MONOXIDE × 2 HEC HEME C × 4 Experimental method not declared
NMR measurement conditions pH 5.9；296 K；Ionic strength (raw mmCIF value) 10 MM PHOSPHATE BUFFER；Pressure 1
Resolution not provided
1MDV KEY ROLE OF PHENYLALANINE 20 IN CYTOCHROME C3: STRUCTURE, STABILITY AND FUNCTION STUDIES Deposited 1998-09-08 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 23–129（107 aa）
Mutation：F20L HEM PROTOPORPHYRIN IX CONTAINING FE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.6；pH 7.6
Resolution 2.30 Å R-free 0.296
1MDV KEY ROLE OF PHENYLALANINE 20 IN CYTOCHROME C3: STRUCTURE, STABILITY AND FUNCTION STUDIES Deposited 1998-09-08 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 23–129（107 aa）
Mutation：F20L HEM PROTOPORPHYRIN IX CONTAINING FE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.6；pH 7.6
Resolution 2.30 Å R-free 0.296
1MDV KEY ROLE OF PHENYLALANINE 20 IN CYTOCHROME C3: STRUCTURE, STABILITY AND FUNCTION STUDIES Deposited 1998-09-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric
Chain A 23–129（107 aa）
Chain B 23–129（107 aa）
Mutation：F20L Mutation：F20L HEM PROTOPORPHYRIN IX CONTAINING FE × 32 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.6；pH 7.6
Resolution 2.30 Å R-free 0.296
2CTH CYTOCHROME C3 FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH Deposited 1997-06-18 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 23–129（107 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；PROTEIN WAS CRYSTALLIZED FROM 75% (V/V) ETHANOL AND 0.05 M SODIUM ACETATE (PH 5.5)
Resolution 1.67 Å R-free 0.190
2CTH CYTOCHROME C3 FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH Deposited 1997-06-18 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 23–129（107 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；PROTEIN WAS CRYSTALLIZED FROM 75% (V/V) ETHANOL AND 0.05 M SODIUM ACETATE (PH 5.5)
Resolution 1.67 Å R-free 0.190
2CYM EFFECTS OF AMINO ACID SUBSTITUTION ON THREE-DIMENSIONAL STRUCTURE: AN X-RAY ANALYSIS OF CYTOCHROME C3 FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH AT 2 ANGSTROMS RESOLUTION Deposited 1993-09-29 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 23–129（107 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 4 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å

5 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CYC3_DESVH
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–107； UniProt 23–129

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 2bpn

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2bpn
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2bpn
Deposition date deposition_date2005-04-21
Structure title titleSOLUTION STRUCTURE OF DESULFOVIBRIO VULGARIS (HILDENBOROUGH) FERRICYTOCHROME C3, NMR, 20 STRUCTURES
Keywords keywordsELECTRON TRANSPORT, HEMEPROTEIN, CYTOCHROME C3, REDOX COOPERATIVITY, REDOX-BOHR COOPERATIVITY, TRANSDUCTION, PARAMAGNETIC; ELECTRON TRANSPORT
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier13.54 Å
Radius of gyration Rg (electron density) rg_electron13.70 Å
Forward intensity I(0) i01139680000.00
Molecular weight molecular_weight282450.0 kDa
Excluded volume excluded_volume349930 ų
Envelope volume envelope_volume27332 ų
Hydration-shell volume shell_volume14901 ų
Envelope diameter envelope_diameter51.5 Å
Shell Rg shell_rg21.28 Å
Envelope Rg envelope_rg15.63 Å
Shape Rg shape_rg13.67 Å
Total Rg total_rg13.93 Å
Total atoms total_atoms38000
Residues n_residues2140
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 dmax41.5 Å
Rg (real space) rg_real13.46 Å
Rg uncertainty (real space) rg_real_error0.25 Å
I(0) (real space) i0_real1.1400e+09
I(0) uncertainty (real space) i0_real_error1.2920e+07
Rg (reciprocal space) rg_reciprocal13.46 Å
I(0) (reciprocal space) i0_reciprocal1140000000.0000
Solution quality estimate total_estimate0.8667
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary18.4 Å
Skewness Skewness skewness0.142
Kurtosis Kurtosis kurtosis-0.342
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha362000.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.914; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.529
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd2bpna_
Class classa — All alpha proteins
Fold Fold folda.138 — Multiheme cytochromes
Superfamily Superfamily superfamilya.138.1 — Multiheme cytochromes
Family Family familya.138.1.1 — Cytochrome c3-like

CATH v4.4 (1 domains)

Domain ID domain_id2bpnA00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology10 — Cytochrome C3
Homologous superfamily homologous superfamily10 — Cytochrome C3
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8. Citations (3)

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9. Files and Curves (10)