5l31

Crystal structure of an engineered metal-free RIDC1 variant containing five disulfide bonds.

Method: X-RAY DIFFRACTION Dmax: 64.3 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 Fragment:UNP residues 23-128 Fragment:UNP residues 23-128 Non-standard monomer:Yes (specific site not provided by mmCIF) HEC HEME C × 4 NA SODIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;293 K;Drop consists of 1 uL of 45% MPD, and 0.1 M Bis Tris (pH 6.5) mixed with 1.5 uL of 2.8 mM protein Resolution 2.40 Å R-free 0.267

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, 2
Chains and sequence ranges Author chain A; PDBConstruct 1–106; UniProt 23–128 Author chain C; PDBConstruct 1–106; UniProt 23–128 Author chain D; PDBConstruct 1–106; UniProt 23–128 Author chain B; 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 5l31

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5l31
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id5l31
Deposition date deposition_date2016-08-02
Structure title titleCrystal structure of an engineered metal-free RIDC1 variant containing five disulfide bonds.
Keywords keywordsengineered protein, cytochrome, complex, 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_guinier22.17
Radius of gyration Rg (electron density) rg_electron20.99
Forward intensity I(0) i043001600.00
Molecular weight molecular_weight48664.0 kDa
Excluded volume excluded_volume59909 ų
Envelope volume envelope_volume71325 ų
Hydration-shell volume shell_volume27293 ų
Envelope diameter envelope_diameter66.0
Shell Rg shell_rg28.44
Envelope Rg envelope_rg21.04
Shape Rg shape_rg20.97
Total Rg total_rg21.92
Total atoms total_atoms3396
Residues n_residues418
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 dmax64.3
Rg (real space) rg_real21.93
Rg uncertainty (real space) rg_real_error0.19
I(0) (real space) i0_real4.3000e+07
I(0) uncertainty (real space) i0_real_error4.3890e+05
Rg (reciprocal space) rg_reciprocal21.98
I(0) (reciprocal space) i0_reciprocal43000000.0000
Solution quality estimate total_estimate0.9043
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.7
Skewness Skewness skewness0.011
Kurtosis Kurtosis kurtosis-0.502
Angular range angular_range— – 0.3600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha16110000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.937; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.967; Smooth: 0.972

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd5l31a_
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_idd5l31b_
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_idd5l31c_
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_idd5l31d_
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)