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351c

STRUCTURE OF CYTOCHROME C551 FROM P. AERUGINOSA REFINED AT 1.6 ANGSTROMS RESOLUTION AND COMPARISON OF THE TWO REDOX FORMS

Method: X-RAY DIFFRACTION Dmax: 38.3 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

CYTOCHROME C551

Pseudomonas aeruginosa

UniProt P00099

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 23–104 Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 1.60 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 351C Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1DVV SOLUTION STRUCTURE OF THE QUINTUPLE MUTANT OF CYTOCHROME C-551 FROM PSEUDOMONAS AERUGINOSA Deposited 2000-01-22 Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 23–104（82 aa）
Mutation：F7A, V13M, F34Y, E43Y, V78I HEM PROTOPORPHYRIN IX CONTAINING FE × 1 SOLUTION NMR
NMR measurement conditions pH 5；298 K；Pressure 1
NMR sample composition 1mM cytochrome c551(F7A/V13M/F34Y/E43Y/V78I) reduced with dithionite | 90% H2O/10% D2O
NMR sample composition 1mM cytochrome c551(F7A/V13M/F34Y/E43Y/V78I) reduced with dithionite | 100% D2O
NMR sample composition 1mM cytochrome c551(F7A/V13M/F34Y/E43Y/V78I) U-15N reduced with dithionite | 90% H2O/10% D2O
NMR sample composition 1mM cytochrome c551(F7A/V13M/F34Y/E43Y/V78I) U-15N,13C reduced with dithionite | 90% H2O/10% D2O
Resolution not provided
2EXV Crystal structure of the F7A mutant of the cytochrome c551 from Pseudomonas aeruginosa Deposited 2005-11-09 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 23–104（82 aa）
Mutation：F7A HEC HEME C × 1 ACY ACETIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；294 K；26-30% PEG 4K, zinc acetate 0.2 M, sodium acetate 0.1 M, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Resolution 1.86 Å R-free 0.233
2EXV Crystal structure of the F7A mutant of the cytochrome c551 from Pseudomonas aeruginosa Deposited 2005-11-09 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 23–104（82 aa）
Mutation：F7A HEC HEME C × 1 ACY ACETIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；294 K；26-30% PEG 4K, zinc acetate 0.2 M, sodium acetate 0.1 M, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Resolution 1.86 Å R-free 0.233
2PAC SOLUTION STRUCTURE OF FE(II) CYTOCHROME C551 FROM PSEUDOMONAS AERUGINOSA AS DETERMINED BY TWO-DIMENSIONAL 1H NMR Deposited 1993-05-05 Different ligand/ion Different experimental method Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 23–104（82 aa）
Not recorded HEC HEME C × 1 SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
3X39 Domain-swapped dimer of Pseudomonas aeruginosa cytochrome c551 Deposited 2015-01-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 23–104（82 aa） Fragment：UNP residues 23-104
Not recorded HEC HEME C × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.1M HEPES-NaOH buffer containing 1.4M sodium citrate tribasic dehydrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.50 Å R-free 0.188
3X39 Domain-swapped dimer of Pseudomonas aeruginosa cytochrome c551 Deposited 2015-01-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 23–104（82 aa） Fragment：UNP residues 23-104
Not recorded HEC HEME C × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.1M HEPES-NaOH buffer containing 1.4M sodium citrate tribasic dehydrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.50 Å R-free 0.188
451C STRUCTURE OF CYTOCHROME C551 FROM P. AERUGINOSA REFINED AT 1.6 ANGSTROMS RESOLUTION AND COMPARISON OF THE TWO REDOX FORMS Deposited 1981-07-20 Parsed fields agree Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 23–104（82 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.60 Å
5XEC Heterodimer constructed from PA cyt c551-HT cyt c552 and HT cyt c552-PA cyt c551 chimeric proteins Deposited 2017-04-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 23–42（20 aa） Fragment：UNP RESIDUES 23-42,UNP RESIDUES 37-98
Chain C 43–104（62 aa） Fragment：UNP RESIDUES 19-36,UNP RESIDUES 43-104
Not recorded HEC HEME C × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；100 mM Tris-HCl containing 200 mM sodium acetate, 30% w/v PEG 4000
Resolution 1.10 Å R-free 0.197
5XED Heterodimer constructed from M61A PA cyt c551-HT cyt c552 and HT cyt c552-PA cyt c551 chimeric proteins Deposited 2017-04-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 23–42（20 aa） Fragment：UNP RESIDUES 23-42,UNP RESIDUES 37-98
Chain C 43–104（62 aa） Fragment：UNP RESIDUES 19-36,UNP RESIDUES 43-104
Mutation：M61A HEC HEME C × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；100 mM MES containing 25% w/v PEG 6000
Resolution 1.55 Å R-free 0.238

7 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CY551_PSEAE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–82； UniProt 23–104

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 351c

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 351c
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2. Structure Basics 2. Structure Basics

Entry ID entry_id351c
Deposition date deposition_date1981-07-20
Structure title titleSTRUCTURE OF CYTOCHROME C551 FROM P. AERUGINOSA REFINED AT 1.6 ANGSTROMS RESOLUTION AND COMPARISON OF THE TWO REDOX FORMS
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_guinier12.62 Å
Radius of gyration Rg (electron density) rg_electron11.30 Å
Forward intensity I(0) i01823800.00
Molecular weight molecular_weight9310.0 kDa
Excluded volume excluded_volume11655 ų
Envelope volume envelope_volume12124 ų
Hydration-shell volume shell_volume9196 ų
Envelope diameter envelope_diameter36.0 Å
Shell Rg shell_rg16.95 Å
Envelope Rg envelope_rg11.57 Å
Shape Rg shape_rg11.27 Å
Total Rg total_rg12.73 Å
Total atoms total_atoms653
Residues n_residues82
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 dmax38.3 Å
Rg (real space) rg_real12.52 Å
Rg uncertainty (real space) rg_real_error0.19 Å
I(0) (real space) i0_real1.8240e+06
I(0) uncertainty (real space) i0_real_error1.9120e+04
Rg (reciprocal space) rg_reciprocal12.52 Å
I(0) (reciprocal space) i0_reciprocal1824000.0000
Solution quality estimate total_estimate0.8959
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary16.5 Å
Skewness Skewness skewness0.030
Kurtosis Kurtosis kurtosis-0.382
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha395100.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.897; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.977
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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_idd351ca_
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_id351cA00
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 (3)

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9. Files and Curves (10)