2FV8 | pdb_00002fv8

The crystal structure of RhoB in the GDP-bound state

PDB DOI: https://doi.org/10.2210/pdb2FV8/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2006-01-30 Released: 2006-02-28
Deposition Author(s): Turnbull, A.P., Soundararajan, M., Smee, C., Johansson, C., Schoch, G., Gorrec, F., Bray, J., Papagrigoriou, E., von Delft, F., Weigelt, J., Edwards, A., Arrowsmith, C., Sundstrom, M., Doyle, D., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.253 (Depositor), 0.263 (DCC)
R-Value Work:
0.210 (Depositor), 0.217 (DCC)
R-Value Observed:
0.212 (Depositor)

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

The crystal structure of RhoB in the GDP-bound state

Turnbull, A.P., Soundararajan, M., Smee, C., Johansson, C., Schoch, G., Gorrec, F., Bray, J., Papagrigoriou, E., von Delft, F., Weigelt, J., Edwards, A., Arrowsmith, C., Sundstrom, M., Doyle, D.

To be published.

Macromolecule Content

Total Structure Weight: 24.08 kDa
Atom Count: 1,527
Modeled Residue Count: 180
Deposited Residue Count: 207
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rho-related GTP-binding protein RhoB	A	207	Homo sapiens	Mutation(s): 0 Gene Names: RHOB, ARH6, ARHB
UniProt & NIH Common Fund Data Resources
Find proteins for P62745 (Homo sapiens) Explore P62745 Go to UniProtKB: P62745
PHAROS: P62745 GTEx: ENSG00000143878
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62745
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP Query on GDP Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.253 (Depositor), 0.263 (DCC)
R-Value Work: 0.210 (Depositor), 0.217 (DCC)
R-Value Observed: 0.212 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.519	α = 90
b = 42.233	β = 90.58
c = 33.85	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2006-02-28

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2006-02-28
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.3: 2024-02-14
Changes: Data collection, Database references, Derived calculations
Version 1.4: 2024-04-03
Changes: Refinement description