3GEB | pdb_00003geb

Crystal Structure of edeya2

PDB DOI: https://doi.org/10.2210/pdb3GEB/pdb

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

Deposited: 2009-02-25 Released: 2009-04-07
Deposition Author(s): Kim, S.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.218 (Depositor), 0.215 (DCC)
R-Value Work:
0.171 (Depositor), 0.170 (DCC)
R-Value Observed:
0.176 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Structure of edeya2

Kim, S.J., Jeong, D.G., Jung, S.K., Seong, E.R.

To be published.

Macromolecule Content

Total Structure Weight: 124.31 kDa
Atom Count: 8,355
Modeled Residue Count: 1,025
Deposited Residue Count: 1,096
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Eyes absent homolog 2	A, B, C, D	274	Homo sapiens	Mutation(s): 0 EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for O00167 (Homo sapiens) Explore O00167 Go to UniProtKB: O00167
PHAROS: O00167 GTEx: ENSG00000064655
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O00167
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain H [auth D] SDF format, chain G [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain H [auth D] MOL2 format, chain G [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain H [auth D] mmCIF format, chain G [auth C]	E [auth A], F [auth B], G [auth C], H [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.218 (Depositor), 0.215 (DCC)
R-Value Work: 0.171 (Depositor), 0.170 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 183.612	α = 90
b = 183.612	β = 90
c = 120.15	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
SOLVE	phasing
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-04-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-04-07
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-03-20
Changes: Data collection, Database references, Derived calculations

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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.