4E71 | pdb_00004e71

Crystal structure of the RHO GTPASE binding domain of Plexin B2

PDB DOI: https://doi.org/10.2210/pdb4E71/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2012-03-16 Released: 2012-03-28
Deposition Author(s): Guan, X., Wang, H., Tempel, W., Tong, Y., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Park, H., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.26 Å
R-Value Free:
0.285 (Depositor), 0.298 (DCC)
R-Value Work:
0.244 (Depositor), 0.244 (DCC)
R-Value Observed:
0.246 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of the RHO GTPASE binding domain of Plexin B2

Guan, X., Wang, H., Tempel, W., Tong, Y., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Park, H.

To be published.

Macromolecule Content

Total Structure Weight: 12.37 kDa
Atom Count: 660
Modeled Residue Count: 90
Deposited Residue Count: 111
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Plexin-B2	A	111	Homo sapiens	Mutation(s): 0 Gene Names: PLXNB2, KIAA0315
UniProt & NIH Common Fund Data Resources
Find proteins for O15031 (Homo sapiens) Explore O15031 Go to UniProtKB: O15031
PHAROS: O15031 GTEx: ENSG00000196576
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O15031
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NA Query on NA 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]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.26 Å
R-Value Free: 0.285 (Depositor), 0.298 (DCC)
R-Value Work: 0.244 (Depositor), 0.244 (DCC)
R-Value Observed: 0.246 (Depositor)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.38	α = 90
b = 48.38	β = 90
c = 157.36	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
BUSTER	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-03-28

Deposition Author(s):

Arrowsmith, C.H.

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2012-03-28
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.