2FW2 | pdb_00002fw2

Catalytic domain of CDY

PDB DOI: https://doi.org/10.2210/pdb2FW2/pdb

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

Deposited: 2006-01-31 Released: 2006-02-14
Deposition Author(s): Min, J.R., Antoshenko, T., Wu, H., Weigelt, J., Sundstrom, M., Arrowsmith, C., Edwards, A.M., Bochkarev, A., Plotnikov, A.N., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.253 (Depositor), 0.187 (DCC)
R-Value Work:
0.185 (Depositor), 0.187 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 2FW2

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

Literature

The Crystal Structure of catalytic domain of Human Testis-specific chromodomain protein Y.

Min, J.R., Antoshenko, T., Wu, H., Weigelt, J., Sundstrom, M., Arrowsmith, C., Edwards, A.M., Bochkarev, A., Plotnikov, A.N.

To be published.

Macromolecule Content

Total Structure Weight: 173.29 kDa
Atom Count: 12,641
Modeled Residue Count: 1,545
Deposited Residue Count: 1,560
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Testis-specific chromodomain protein Y 2	A, B, C, D, E A, B, C, D, E, F	260	Homo sapiens	Mutation(s): 0 Gene Names: CDY2A, CDY2 EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6F7 (Homo sapiens) Explore Q9Y6F7 Go to UniProtKB: Q9Y6F7
PHAROS: Q9Y6F7 GTEx: ENSG00000182415 ENSG00000129873
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y6F7
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.253 (Depositor), 0.187 (DCC)
R-Value Work: 0.185 (Depositor), 0.187 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.454	α = 90
b = 133.579	β = 117.56
c = 82.328	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2006-02-14

Deposition Author(s):

Plotnikov, A.N.

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2006-02-14
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Derived calculations, Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2023-08-30
Changes: Data collection, Database references, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.