6sup

Crystal Structure of TcdB2-TccC3-Cdc42

Method: X-RAY DIFFRACTION Dmax: 149.6 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

TcdB2,TccC3,Cell division control protein 42 homolog

Homo sapiens

UniProt P60953

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 167–179 Not recorded MG MAGNESIUM ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 4.6;293.15 K;0.1 M sodium chloride, 0.1 M magnesium chloride, 0.1 M tri-sodium citrate pH 5.5, 12 % PEG 4000 Seeding: 0.1 M magnesium chloride, 0.1 M tri-sodium acetate pH 4.6, 12 % PEG 6000 Resolution 2.00 Å R-free 0.320

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.

45 other PDB entries and 68 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CDC42_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2116–2128; UniProt 167–179

TcdB2,TccC3,Cell division control protein 42 homolog

Homo sapiens

UniProt Q8GF97

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 35–678 Not recorded MG MAGNESIUM ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 4.6;293.15 K;0.1 M sodium chloride, 0.1 M magnesium chloride, 0.1 M tri-sodium citrate pH 5.5, 12 % PEG 4000 Seeding: 0.1 M magnesium chloride, 0.1 M tri-sodium acetate pH 4.6, 12 % PEG 6000 Resolution 2.00 Å R-free 0.320

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.

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q8GF97_PHOLU
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1472–2115; UniProt 35–678

TcdB2,TccC3,Cell division control protein 42 homolog

Homo sapiens

UniProt Q8GF99

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 32–1471 Not recorded MG MAGNESIUM ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 4.6;293.15 K;0.1 M sodium chloride, 0.1 M magnesium chloride, 0.1 M tri-sodium citrate pH 5.5, 12 % PEG 4000 Seeding: 0.1 M magnesium chloride, 0.1 M tri-sodium acetate pH 4.6, 12 % PEG 6000 Resolution 2.00 Å R-free 0.320

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.

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q8GF99_PHOLU
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–1440; UniProt 32–1471

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 6sup

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id6sup
Deposition date deposition_date2019-09-16
Structure title titleCrystal Structure of TcdB2-TccC3-Cdc42
Keywords keywordsToxins, Tc Toxins, TOXIN; TOXIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier44.12
Radius of gyration Rg (electron density) rg_electron43.66
Forward intensity I(0) i0908701000.00
Molecular weight molecular_weight240590.0 kDa
Excluded volume excluded_volume298070 ų
Envelope volume envelope_volume424190 ų
Hydration-shell volume shell_volume82061 ų
Envelope diameter envelope_diameter164.6
Shell Rg shell_rg48.60
Envelope Rg envelope_rg41.95
Shape Rg shape_rg43.64
Total Rg total_rg43.97
Total atoms total_atoms17004
Residues n_residues2128
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 dmax149.6
Rg (real space) rg_real44.11
Rg uncertainty (real space) rg_real_error1.43
I(0) (real space) i0_real9.0870e+08
I(0) uncertainty (real space) i0_real_error1.6080e+07
Rg (reciprocal space) rg_reciprocal44.12
I(0) (reciprocal space) i0_reciprocal908700000.0000
Solution quality estimate total_estimate0.8619
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary54.0
Skewness Skewness skewness0.385
Kurtosis Kurtosis kurtosis-0.164
Angular range angular_range— – 0.1800 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha71240000.0000
Real-space data points n_real_points37
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.773; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.881

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id6supA01
Class class2 — Mainly Beta
Architecture architecture180 — Shell
Topology topology10 — RHS repeat-associated core
Homologous superfamily homologous superfamily10 — RHS repeat-associated core

8. Citations (1)

9. Files and Curves (10)