4u9e

Crystal structure of the Zn-directed tetramer of the engineered cyt cb562 variant, A104/57G AB3

Method: X-RAY DIFFRACTION Dmax: 47.5 Å Quality: GOOD

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 Fragment:UNP residues 23-128 Mutation:R34A, L38A, Q41W, K42S, E57G, K59H, D66W, V69I, D73H, K77H, A89H, T96C, R98C, A100H, Y101C, K104A, HEC HEME C × 4 CA CALCIUM ION × 20 ZN ZINC ION × 8 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;298 K;27% (+/-)-2-methyl-2,4-pentanediol 400 in 100 mM Bis-Tris (pH 6.5) with 0.2M CaCl2 and 20 mM ampicillin Resolution 2.80 Å R-free 0.285

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

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 4u9e

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4u9e
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4u9e
Deposition date deposition_date2014-08-06
Structure title titleCrystal structure of the Zn-directed tetramer of the engineered cyt cb562 variant, A104/57G AB3
Keywords keywordsdesigned enzyme, Zn-coordinating protein, tetramer assembly, ELECTRON TRANSPORT; ELECTRON TRANSPORT
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier14.52
Radius of gyration Rg (electron density) rg_electron13.28
Forward intensity I(0) i02840220.00
Molecular weight molecular_weight11111.0 kDa
Excluded volume excluded_volume13563 ų
Envelope volume envelope_volume15354 ų
Hydration-shell volume shell_volume10229 ų
Envelope diameter envelope_diameter46.3
Shell Rg shell_rg18.46
Envelope Rg envelope_rg13.49
Shape Rg shape_rg13.21
Total Rg total_rg14.58
Total atoms total_atoms762
Residues n_residues91
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 dmax47.5
Rg (real space) rg_real14.46
Rg uncertainty (real space) rg_real_error0.25
I(0) (real space) i0_real2.8400e+06
I(0) uncertainty (real space) i0_real_error3.1730e+04
Rg (reciprocal space) rg_reciprocal14.47
I(0) (reciprocal space) i0_reciprocal2840000.0000
Solution quality estimate total_estimate0.8864
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary17.4
Skewness Skewness skewness0.234
Kurtosis Kurtosis kurtosis-0.300
Angular range angular_range— – 0.5000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha385800.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.846; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.983

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd4u9ea_
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 (1 domains)

Domain ID domain_id4u9eA00
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)