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3m97

Structure of the soluble domain of cytochrome c552 with its flexible linker segment from Paracoccus denitrificans

Method: X-RAY DIFFRACTION Dmax: 51.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Cytochrome c-552

Paracoccus denitrificans

UniProt P54820

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 X； UniProt 38–176 Fragment：soluble domain with flexible linker segment (UNP residues 38-176) HEC HEME C × 1 ZN ZINC ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；20 % PEG 550 MME, 0.1 M Zinc sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 1.33 Å R-free 0.229

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 3M97 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1C7M SOLUTION STRUCTURE OF THE FUNCTIONAL DOMAIN OF PARACOCCUS DENITRIFICANS CYTOCHROME C552 IN THE REDUCED STATE Deposited 2000-03-03 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 78–176（99 aa） Fragment：SOLUBLE FUNCTIONAL DOMAIN
Not recorded HEC HEME C × 1 SOLUTION NMR
NMR measurement conditions pH 5.5；298 K
NMR sample composition 20 MM PHOSPHATE, 90% H2O/ 10% D2O
Resolution not provided
1I6D SOLUTION STRUCTURE OF THE FUNCTIONAL DOMAIN OF PARACOCCUS DENITRIFICANS CYTOCHROME C552 IN THE REDUCED STATE Deposited 2001-03-02 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 78–176（99 aa） Fragment：SOLUBLE FUNCTIONAL DOMAIN
Not recorded HEC HEME C × 1 SOLUTION NMR
NMR measurement conditions pH 5.5；298 K
NMR sample composition 20 MM PHOSPHATE, 90% H2O/ 10% D2O
Resolution not provided
1I6E SOLUTION STRUCTURE OF THE FUNCTIONAL DOMAIN OF PARACOCCUS DENITRIFICANS CYTOCHROME C552 IN THE OXIDIZED STATE Deposited 2001-03-02 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 78–176（99 aa） Fragment：SOLUBLE FUNCTIONAL DOMAIN
Not recorded HEC HEME C × 1 SOLUTION NMR
NMR measurement conditions pH 5.5；298 K
NMR sample composition 20 MM PHOSPHATE, 90% H2O/ 10% D2O
Resolution not provided
1QL3 Structure of the soluble domain of cytochrome c552 from Paracoccus denitrificans in the reduced state Deposited 1999-08-20 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 78–176（99 aa） Fragment：SOLUBLE DOMAIN
Not recorded HEC HEME C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.5；pH 4.50
Resolution 1.40 Å R-free 0.242
1QL3 Structure of the soluble domain of cytochrome c552 from Paracoccus denitrificans in the reduced state Deposited 1999-08-20 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 78–176（99 aa） Fragment：SOLUBLE DOMAIN
Not recorded HEC HEME C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.5；pH 4.50
Resolution 1.40 Å R-free 0.242
1QL3 Structure of the soluble domain of cytochrome c552 from Paracoccus denitrificans in the reduced state Deposited 1999-08-20 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 78–176（99 aa） Fragment：SOLUBLE DOMAIN
Not recorded HEC HEME C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.5；pH 4.50
Resolution 1.40 Å R-free 0.242
1QL3 Structure of the soluble domain of cytochrome c552 from Paracoccus denitrificans in the reduced state Deposited 1999-08-20 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 78–176（99 aa） Fragment：SOLUBLE DOMAIN
Not recorded HEC HEME C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.5；pH 4.50
Resolution 1.40 Å R-free 0.242
1QL4 Structure of the soluble domain of cytochrome c552 from Paracoccus denitrificans in the oxidised state Deposited 1999-08-20 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 78–176（99 aa） Fragment：SOLUBLE DOMAIN
Not recorded HEC HEME C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.5；pH 4.50
Resolution 1.50 Å R-free 0.268
1QL4 Structure of the soluble domain of cytochrome c552 from Paracoccus denitrificans in the oxidised state Deposited 1999-08-20 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 78–176（99 aa） Fragment：SOLUBLE DOMAIN
Not recorded HEC HEME C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.5；pH 4.50
Resolution 1.50 Å R-free 0.268
1QL4 Structure of the soluble domain of cytochrome c552 from Paracoccus denitrificans in the oxidised state Deposited 1999-08-20 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 78–176（99 aa） Fragment：SOLUBLE DOMAIN
Not recorded HEC HEME C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.5；pH 4.50
Resolution 1.50 Å R-free 0.268
1QL4 Structure of the soluble domain of cytochrome c552 from Paracoccus denitrificans in the oxidised state Deposited 1999-08-20 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 78–176（99 aa） Fragment：SOLUBLE DOMAIN
Not recorded HEC HEME C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.5；pH 4.50
Resolution 1.50 Å R-free 0.268

5 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CY552_PARDE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain X； PDBConstruct 2–140； UniProt 38–176

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 3m97

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3m97
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3m97
Deposition date deposition_date2010-03-20
Structure title titleStructure of the soluble domain of cytochrome c552 with its flexible linker segment from Paracoccus denitrificans
Keywords keywords;Electron transport chain (cytochrome), Electron transfer, P. denitrificans, electron donor, Cell membrane, Electron transport, Heme, Iron, Membrane, Metal-binding, Transmembrane, 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_guinier15.43 Å
Radius of gyration Rg (electron density) rg_electron13.80 Å
Forward intensity I(0) i03820200.00
Molecular weight molecular_weight13195.0 kDa
Excluded volume excluded_volume16161 ų
Envelope volume envelope_volume18560 ų
Hydration-shell volume shell_volume11567 ų
Envelope diameter envelope_diameter51.6 Å
Shell Rg shell_rg19.49 Å
Envelope Rg envelope_rg14.38 Å
Shape Rg shape_rg13.72 Å
Total Rg total_rg15.17 Å
Total atoms total_atoms913
Residues n_residues118
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 dmax51.9 Å
Rg (real space) rg_real15.38 Å
Rg uncertainty (real space) rg_real_error0.32 Å
I(0) (real space) i0_real3.8200e+06
I(0) uncertainty (real space) i0_real_error4.7770e+04
Rg (reciprocal space) rg_reciprocal15.38 Å
I(0) (reciprocal space) i0_reciprocal3820000.0000
Solution quality estimate total_estimate0.8711
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary19.1 Å
Skewness Skewness skewness0.270
Kurtosis Kurtosis kurtosis-0.234
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha636000.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.778; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.991
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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) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id3m97X00
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)