3EO2 | pdb_00003eo2

Crystal structure of the RhoGEF domain of human neuroepithelial cell-transforming gene 1 protein

PDB DOI: https://doi.org/10.2210/pdb3EO2/pdb

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

Deposited: 2008-09-26 Released: 2008-10-07
Deposition Author(s): Nedyalkova, L., Tong, Y., Tempel, W., MacKenzie, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.250 (Depositor), 0.257 (DCC)
R-Value Work:
0.213 (Depositor), 0.242 (DCC)
R-Value Observed:
0.215 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of the RhoGEF domain of human neuroepithelial cell-transforming gene 1 protein

Nedyalkova, L., Tong, Y., Tempel, W., MacKenzie, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Park, H.

To be published.

Macromolecule Content

Total Structure Weight: 27.07 kDa
Atom Count: 1,469
Modeled Residue Count: 187
Deposited Residue Count: 231
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuroepithelial cell-transforming gene 1 protein	A	231	Homo sapiens	Mutation(s): 0 Gene Names: NET1, ARHGEF8
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z628 (Homo sapiens) Explore Q7Z628 Go to UniProtKB: Q7Z628
PHAROS: Q7Z628 GTEx: ENSG00000173848
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7Z628
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UNX Query on UNX 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]	UNKNOWN ATOM OR ION X		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.250 (Depositor), 0.257 (DCC)
R-Value Work: 0.213 (Depositor), 0.242 (DCC)
R-Value Observed: 0.215 (Depositor)

Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.629	α = 90
b = 95.629	β = 90
c = 62.887	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-10-07

Deposition Author(s):

Arrowsmith, C.H.

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2008-10-07
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2020-10-14
Changes: Data collection, Database references, Derived calculations
Version 1.4: 2023-09-06
Changes: Data collection, Database references, 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.