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1qyz

Characterization of the malformed, recombinant cytochrome rC552

Method: X-RAY DIFFRACTION Dmax: 46.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Cytochrome c-552

Thermus thermophilus

UniProt P04164

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 18–148 Not recorded HCO 2-ACETYL-PROTOPORPHYRIN IX × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.3；298 K；PEG 5K MME, imidazole-malate buffer, NaCl, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 298K Resolution 1.40 Å R-free 0.260

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 1QYZ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1C52 THERMUS THERMOPHILUS CYTOCHROME-C552: A NEW HIGHLY THERMOSTABLE CYTOCHROME-C STRUCTURE OBTAINED BY MAD PHASING Deposited 1997-06-23 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 18–148（131 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.2；PROTEIN WAS CRYSTALLIZED FROM 2.8 M AMMONIUM SULFATE, 100 MM TRIS/HCL, PH 8.2
Resolution 1.28 Å R-free 0.224
1FOC Cytochrome C557: improperly folded thermus thermophilus C552 Deposited 2000-08-27 Different construct Different mutation/modification 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 17–148（132 aa）
Chain B 17–148（132 aa）
Not recorded HEC HEME C × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；297 K；42-46% MPEG 2K (w/v), 0.1M Na cacodylate pH 7.0, 50mM NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 24K
Resolution 3.00 Å R-free 0.423
1R0Q Characterization of the conversion of the malformed, recombinant cytochrome rc552 to a 2-formyl-4-vinyl (Spirographis) heme Deposited 2003-09-22 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 18–148（131 aa）
Not recorded HFM 2-FORMYL-PROTOPORPHRYN IX × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.3；298 K；MPEG 5K, imidazole-malate buffer, NaCl, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 1.61 Å R-free 0.255
2FWL The cytochrome c552/CuA complex from Thermus thermophilus Deposited 2006-02-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–131（131 aa）
Not recorded HEC HEME C × 1 CUA DINUCLEAR COPPER ION × 1 SOLUTION NMR
NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 20mM phosphate buffer；Pressure ambient
NMR sample composition 0.5mM cytochrome c552 U-15N, 20mM phosphate buffer, 2mM CuA domain, 95% H2O, 5% D2O | 95% H2O/5% D2O
NMR sample composition 0.5mM CuA domain U-15N, 20mM phosphate buffer, 2mM cytochrome c552, 95% H2O, 5% D2O | 95% H2O/5% D2O
Resolution not provided
3VNW Crystal structure of cytochrome c552 from Thermus thermophilus at pH 5.44 Deposited 2012-01-18 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 3–131（129 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.44；298 K；0.2M Imidazole-Malate, 42% MPEG 5K, pH 5.44, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 1.97 Å R-free 0.232

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

View Construct and Data Evidence
UniProt name C552_THETH
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–131； UniProt 18–148

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 1qyz

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1qyz
Deposition date deposition_date2003-09-12
Structure title titleCharacterization of the malformed, recombinant cytochrome rC552
Keywords keywordsmalformed cytochrome c, OXIDOREDUCTASE; OXIDOREDUCTASE
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_guinier14.90 Å
Radius of gyration Rg (electron density) rg_electron13.50 Å
Forward intensity I(0) i03904480.00
Molecular weight molecular_weight14686.0 kDa
Excluded volume excluded_volume18722 ų
Envelope volume envelope_volume20290 ų
Hydration-shell volume shell_volume12514 ų
Envelope diameter envelope_diameter45.1 Å
Shell Rg shell_rg19.65 Å
Envelope Rg envelope_rg13.89 Å
Shape Rg shape_rg13.45 Å
Total Rg total_rg14.96 Å
Total atoms total_atoms1033
Residues n_residues130
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 dmax46.2 Å
Rg (real space) rg_real14.76 Å
Rg uncertainty (real space) rg_real_error0.27 Å
I(0) (real space) i0_real3.9040e+06
I(0) uncertainty (real space) i0_real_error4.2330e+04
Rg (reciprocal space) rg_reciprocal14.77 Å
I(0) (reciprocal space) i0_reciprocal3904000.0000
Solution quality estimate total_estimate0.8818
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary21.1 Å
Skewness Skewness skewness0.027
Kurtosis Kurtosis kurtosis-0.394
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1136000.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.837; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.967
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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_idd1qyza_
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_id1qyzA00
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)