2jhw

CRYSTAL STRUCTURE OF RHOGDI E155A, E157A MUTANT

Method: X-RAY DIFFRACTION Dmax: 64.3 Å Quality: EXCELLENT

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

RHO GDP-DISSOCIATION INHIBITOR 1

HOMO SAPIENS

UniProt P52565

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 66–201 Fragment:ISOPRENYL-BINDING DOMAIN, RESIDUES 66-201 Mutation:YES SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:pH 8;2M AMMONIUM SULFATE, pH 8.00 Resolution 2.50 Å R-free 0.261
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 66–201 Fragment:ISOPRENYL-BINDING DOMAIN, RESIDUES 66-201 Mutation:YES SO4 SULFATE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:pH 8;2M AMMONIUM SULFATE, pH 8.00 Resolution 2.50 Å R-free 0.261

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.

20 other PDB entries and 52 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GDIR_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 3–138; UniProt 66–201 Author chain B; PDBConstruct 3–138; UniProt 66–201

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 2jhw

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2jhw
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2jhw
Deposition date deposition_date2007-02-23
Structure title titleCRYSTAL STRUCTURE OF RHOGDI E155A, E157A MUTANT
Keywords keywordsSURFACE ENTROPY REDUCTION, INHIBITOR, GTPASE ACTIVATION, CRYSTAL ENGINEERING; INHIBITOR
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier21.60
Radius of gyration Rg (electron density) rg_electron20.34
Forward intensity I(0) i017651400.00
Molecular weight molecular_weight31766.0 kDa
Excluded volume excluded_volume39851 ų
Envelope volume envelope_volume48840 ų
Hydration-shell volume shell_volume20236 ų
Envelope diameter envelope_diameter65.4
Shell Rg shell_rg26.43
Envelope Rg envelope_rg20.44
Shape Rg shape_rg20.25
Total Rg total_rg21.50
Total atoms total_atoms2229
Residues n_residues276
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_real21.45
Rg uncertainty (real space) rg_real_error0.34
I(0) (real space) i0_real1.7650e+07
I(0) uncertainty (real space) i0_real_error2.2240e+05
Rg (reciprocal space) rg_reciprocal21.48
I(0) (reciprocal space) i0_reciprocal17650000.0000
Solution quality estimate total_estimate0.9158
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.4
Skewness Skewness skewness0.061
Kurtosis Kurtosis kurtosis-0.652
Angular range angular_range— – 0.3700 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2717000.0000
Real-space data points n_real_points69
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.973; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.987

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2jhwa_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.18 — E set domains
Family Family familyb.1.18.8 — RhoGDI-like
Domain ID domain_idd2jhwb_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.18 — E set domains
Family Family familyb.1.18.8 — RhoGDI-like

CATH v4.4 (2 domains)

Domain ID domain_id2jhwA00
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology50 — Coagulation Factor XIII; Chain A, domain 1
Homologous superfamily homologous superfamily30 — Coagulation Factor XIII, subunit A, domain 1
Domain ID domain_id2jhwB00
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology50 — Coagulation Factor XIII; Chain A, domain 1
Homologous superfamily homologous superfamily30 — Coagulation Factor XIII, subunit A, domain 1

8. Citations (1)

9. Files and Curves (10)