6dyd

Cu(II)-bound structure of the engineered cyt cb562 variant, CH3

Method: X-RAY DIFFRACTION Dmax: 59.1 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 monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 23–128 Mutation:K59W, I67H, Q71H, T96C, T97H, R98C, Y101C CA CALCIUM ION × 2 HEC HEME C × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.5;293 K;Drop consists of 2 uL of 45% MPD, 200 mM calcium chloride and 0.1 M Bis-Tris (pH 5.5) mixed with 2 uL of 2 mM protein and 2 mM Copper(II) sulfate Resolution 1.72 Å R-free 0.247
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 23–128 Mutation:K59W, I67H, Q71H, T96C, T97H, R98C, Y101C CA CALCIUM ION × 3 HEC HEME C × 1 CU COPPER (II) ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.5;293 K;Drop consists of 2 uL of 45% MPD, 200 mM calcium chloride and 0.1 M Bis-Tris (pH 5.5) mixed with 2 uL of 2 mM protein and 2 mM Copper(II) sulfate Resolution 1.72 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 821 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 6dyd

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id6dyd
Deposition date deposition_date2018-07-01
Structure title titleCu(II)-bound structure of the engineered cyt cb562 variant, CH3
Keywords keywordsDesigned protein, 4-helix bundle, electron transport, 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_guinier19.10
Radius of gyration Rg (electron density) rg_electron18.27
Forward intensity I(0) i012363000.00
Molecular weight molecular_weight25083.0 kDa
Excluded volume excluded_volume30832 ų
Envelope volume envelope_volume35943 ų
Hydration-shell volume shell_volume16712 ų
Envelope diameter envelope_diameter58.8
Shell Rg shell_rg23.84
Envelope Rg envelope_rg18.38
Shape Rg shape_rg18.24
Total Rg total_rg19.18
Total atoms total_atoms1742
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 dmax59.1
Rg (real space) rg_real19.03
Rg uncertainty (real space) rg_real_error0.34
I(0) (real space) i0_real1.2360e+07
I(0) uncertainty (real space) i0_real_error1.6110e+05
Rg (reciprocal space) rg_reciprocal19.04
I(0) (reciprocal space) i0_reciprocal12360000.0000
Solution quality estimate total_estimate0.9090
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary22.2
Skewness Skewness skewness0.203
Kurtosis Kurtosis kurtosis-0.527
Angular range angular_range— – 0.4150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2845000.0000
Real-space data points n_real_points73
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.943; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.985

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd6dyda_
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_idd6dydc_
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)