2J1L

Crystal Structure of Human Rho-related GTP-binding protein RhoD

PDB DOI: https://doi.org/10.2210/pdb2J1L/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2006-08-14 Released: 2006-09-18
Deposition Author(s): Pike, A.C.W., Johansson, C., Gileadi, C., Niesen, F.H., Sobott, F., Schoch, G., Elkins, J., Smee, C., Gorrec, F., Watt, S., Bray, J., Turnbull, A.P., von Delft, F., Arrowsmith, C., Edwards, A., Weigelt, J., Sundstrom, M., Doyle, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.242 (Depositor), 0.240 (DCC)
R-Value Work:
0.217 (Depositor), 0.220 (DCC)
R-Value Observed:
0.219 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of Human Rho-Related GTP-Binding Protein Rhod

Pike, A.C.W., Johansson, C., Gileadi, C., Niesen, F.H., Sobott, F., Schoch, G., Elkins, J., Smee, C., Gorrec, F., Watt, S., Bray, J., Turnbull, A.P., von Delft, F., Arrowsmith, C., Edwards, A., Weigelt, J., Sundstrom, M., Doyle, D.

To be published.

Macromolecule Content

Total Structure Weight: 24.48 kDa
Atom Count: 1,197
Modelled Residue Count: 157
Deposited Residue Count: 214
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RHO-RELATED GTP-BINDING PROTEIN RHOD	A	214	Homo sapiens	Mutation(s): 0 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for O00212 (Homo sapiens) Explore O00212 Go to UniProtKB: O00212
PHAROS: O00212 GTEx: ENSG00000173156
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O00212
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 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]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.242 (Depositor), 0.240 (DCC)
R-Value Work: 0.217 (Depositor), 0.220 (DCC)
R-Value Observed: 0.219 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.811	α = 90
b = 66.81	β = 90
c = 103.921	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-09-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-09-18
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2018-01-24
Changes: Database references
Version 1.3: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description