7n4g

Co-bound crystal structure of the engineered cyt cb562 variant, AB2-H100A, crystallized in the presence of Co(II)

Method: X-RAY DIFFRACTION Dmax: 60.4 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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 23–128 Chain C; UniProt 23–128 Mutation:K59W, D60H, I67H, Q71H, T96C, T97H, R98C, Y101C, K104H HEC HEME C × 2 CO COBALT (II) ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8;298 K;PEG1500 25%, MgCl2 200 mM, pH 8 EPPS 100 mM Resolution 1.93 Å R-free 0.325

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 C; 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 7n4g

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7n4g
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7n4g
Deposition date deposition_date2021-06-04
Structure title titleCo-bound crystal structure of the engineered cyt cb562 variant, AB2-H100A, crystallized in the presence of Co(II)
Keywords keywordsMetal selectivity, Irving-Williams series, 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_guinier19.15
Radius of gyration Rg (electron density) rg_electron18.31
Forward intensity I(0) i012252900.00
Molecular weight molecular_weight24865.0 kDa
Excluded volume excluded_volume30512 ų
Envelope volume envelope_volume36077 ų
Hydration-shell volume shell_volume16735 ų
Envelope diameter envelope_diameter62.2
Shell Rg shell_rg24.06
Envelope Rg envelope_rg18.44
Shape Rg shape_rg18.31
Total Rg total_rg19.13
Total atoms total_atoms1738
Residues n_residues212
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 dmax60.4
Rg (real space) rg_real19.08
Rg uncertainty (real space) rg_real_error0.36
I(0) (real space) i0_real1.2250e+07
I(0) uncertainty (real space) i0_real_error1.5220e+05
Rg (reciprocal space) rg_reciprocal19.09
I(0) (reciprocal space) i0_reciprocal12250000.0000
Solution quality estimate total_estimate0.8245
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary22.6
Skewness Skewness skewness0.206
Kurtosis Kurtosis kurtosis-0.506
Angular range angular_range— – 0.4150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3055000.0000
Real-space data points n_real_points73
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.907; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

8. Citations (1)

9. Files and Curves (10)