6dyl

Vanadyl-bound structure of the engineered cyt b562 variant, CH3Y*

Method: X-RAY DIFFRACTION Dmax: 83.1 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 monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 23–128 Mutation:M7W, K59W, I67H, G70Y, Q71H, T96C, T97H, Y101A, H102I, R106L V VANADIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.5;293 K;Drop consists of 1 uL of 35% PEP 426, 50 mM Magnesium Chloride and 0.1 M Bis-Tris (pH 5.5) mixed with 1 uL of 4 mM protein and 2.2 mM Vanadyl Sulfate (Anaerobic crystal growth) Resolution 1.69 Å R-free 0.226
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 23–128 Mutation:M7W, K59W, I67H, G70Y, Q71H, T96C, T97H, Y101A, H102I, R106L V VANADIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.5;293 K;Drop consists of 1 uL of 35% PEP 426, 50 mM Magnesium Chloride and 0.1 M Bis-Tris (pH 5.5) mixed with 1 uL of 4 mM protein and 2.2 mM Vanadyl Sulfate (Anaerobic crystal growth) Resolution 1.69 Å R-free 0.226
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain E; UniProt 23–128 Mutation:M7W, K59W, I67H, G70Y, Q71H, T96C, T97H, Y101A, H102I, R106L No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.5;293 K;Drop consists of 1 uL of 35% PEP 426, 50 mM Magnesium Chloride and 0.1 M Bis-Tris (pH 5.5) mixed with 1 uL of 4 mM protein and 2.2 mM Vanadyl Sulfate (Anaerobic crystal growth) Resolution 1.69 Å R-free 0.226
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain G; UniProt 23–128 Mutation:M7W, K59W, I67H, G70Y, Q71H, T96C, T97H, Y101A, H102I, R106L No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.5;293 K;Drop consists of 1 uL of 35% PEP 426, 50 mM Magnesium Chloride and 0.1 M Bis-Tris (pH 5.5) mixed with 1 uL of 4 mM protein and 2.2 mM Vanadyl Sulfate (Anaerobic crystal growth) Resolution 1.69 Å R-free 0.226

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 819 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 C; PDBConstruct 1–106; UniProt 23–128 Author chain E; PDBConstruct 1–106; UniProt 23–128 Author chain G; 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 6dyl

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6dyl
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6dyl
Deposition date deposition_date2018-07-01
Structure title titleVanadyl-bound structure of the engineered cyt b562 variant, CH3Y*
Keywords keywordsDesigned protein, 4-helix bundle, METAL BINDING PROTEIN; METAL BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier25.01
Radius of gyration Rg (electron density) rg_electron24.30
Forward intensity I(0) i037495700.00
Molecular weight molecular_weight46064.0 kDa
Excluded volume excluded_volume57126 ų
Envelope volume envelope_volume72515 ų
Hydration-shell volume shell_volume25430 ų
Envelope diameter envelope_diameter85.9
Shell Rg shell_rg30.86
Envelope Rg envelope_rg24.02
Shape Rg shape_rg24.29
Total Rg total_rg25.10
Total atoms total_atoms6287
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 dmax83.1
Rg (real space) rg_real24.98
Rg uncertainty (real space) rg_real_error0.50
I(0) (real space) i0_real3.7500e+07
I(0) uncertainty (real space) i0_real_error5.3590e+05
Rg (reciprocal space) rg_reciprocal24.99
I(0) (reciprocal space) i0_reciprocal37500000.0000
Solution quality estimate total_estimate0.8881
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary33.0
Skewness Skewness skewness0.306
Kurtosis Kurtosis kurtosis-0.294
Angular range angular_range— – 0.3150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8203000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.857; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.994

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd6dyla_
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_idd6dylc_
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_idd6dyle_
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_idd6dylg_
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

8. Citations (1)

9. Files and Curves (10)