3c63

Tetrameric Cytochrome cb562 (K34/H59/D62/H63/H73/A74/H77) Assembly Stabilized by Interprotein Zinc Coordination

Method: X-RAY DIFFRACTION Dmax: 65.6 Å Quality: EXCELLENT

1. Protein Identity and Related Structures Protein Identity & Related Structures

Soluble cytochrome b562

Escherichia coli

UniProt P0ABE7

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 homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 23–128 Chain B; UniProt 23–128 Chain C; UniProt 23–128 Chain D; UniProt 23–128 Mutation:R34K, K59H, R62D, D73H, D74A, K77H, R98C, Y101C ZN ZINC ION × 4 CA CALCIUM ION × 5 HEM PROTOPORPHYRIN IX CONTAINING FE × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;293 K;12% PEG 400, 200 mM CaCl2, 100 mM TRIS, 1.25 mM ZnCl2, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 1.75 Å R-free 0.247

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.

714 other PDB entries and 822 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name C562_ECOLX
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–106; UniProt 23–128 Author chain B; PDBConstruct 1–106; UniProt 23–128 Author chain C; PDBConstruct 1–106; UniProt 23–128 Author chain D; PDBConstruct 1–106; UniProt 23–128

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 3c63

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3c63
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id3c63
Deposition date deposition_date2008-02-02
Structure title titleTetrameric Cytochrome cb562 (K34/H59/D62/H63/H73/A74/H77) Assembly Stabilized by Interprotein Zinc Coordination
Keywords keywords16-helix bundle, interfacial Zn-coordination, Electron transport, Heme, Iron, Metal-binding, Transport; ELECTRON TRANSPORT
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier22.26
Radius of gyration Rg (electron density) rg_electron21.24
Forward intensity I(0) i044168500.00
Molecular weight molecular_weight49280.0 kDa
Excluded volume excluded_volume60668 ų
Envelope volume envelope_volume72599 ų
Hydration-shell volume shell_volume27592 ų
Envelope diameter envelope_diameter68.1
Shell Rg shell_rg28.62
Envelope Rg envelope_rg21.15
Shape Rg shape_rg21.22
Total Rg total_rg22.15
Total atoms total_atoms3425
Residues n_residues424
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax65.6
Rg (real space) rg_real22.08
Rg uncertainty (real space) rg_real_error0.25
I(0) (real space) i0_real4.4170e+07
I(0) uncertainty (real space) i0_real_error5.3100e+05
Rg (reciprocal space) rg_reciprocal22.12
I(0) (reciprocal space) i0_reciprocal44170000.0000
Solution quality estimate total_estimate0.9037
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.8
Skewness Skewness skewness0.030
Kurtosis Kurtosis kurtosis-0.494
Angular range angular_range— – 0.3550 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha13740000.0000
Real-space data points n_real_points67
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.932; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.967; Smooth: 0.982

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd3c63a_
Class classa — All alpha proteins
Fold Fold folda.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamilya.24.3 — Cytochromes
Family Family familya.24.3.1 — Cytochrome b562
Domain ID domain_idd3c63b_
Class classa — All alpha proteins
Fold Fold folda.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamilya.24.3 — Cytochromes
Family Family familya.24.3.1 — Cytochrome b562
Domain ID domain_idd3c63c_
Class classa — All alpha proteins
Fold Fold folda.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamilya.24.3 — Cytochromes
Family Family familya.24.3.1 — Cytochrome b562
Domain ID domain_idd3c63d_
Class classa — All alpha proteins
Fold Fold folda.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamilya.24.3 — Cytochromes
Family Family familya.24.3.1 — Cytochrome b562

CATH v4.4 (4 domains)

Domain ID domain_id3c63A00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily10 — Cytochrome c/b562
Domain ID domain_id3c63B00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily10 — Cytochrome c/b562
Domain ID domain_id3c63C00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily10 — Cytochrome c/b562
Domain ID domain_id3c63D00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily10 — Cytochrome c/b562

8. Citations (1)

9. Files and Curves (10)