3I3C | pdb_00003i3c

Crystal Structural of CBX5 Chromo Shadow Domain

PDB DOI: https://doi.org/10.2210/pdb3I3C/pdb

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

Deposited: 2009-06-30 Released: 2009-08-18
Deposition Author(s): Amaya, M.F., Li, Z., Li, Y., Kozieradzki, I., Edwards, A.M., Arrowsmith, C.H., Weigelt, J., Bountra, C., Bochkarev, A., Min, J., Ouyang, H., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.48 Å
R-Value Free:
0.303 (Depositor), 0.316 (DCC)
R-Value Work:
0.266 (Depositor), 0.282 (DCC)
R-Value Observed:
0.268 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structural of CBX5 Chromo Shadow Domain

Li, Z., Li, Y., Amaya, M.F., Edwards, A.M., Arrowsmith, C.H., Weigelt, J., Bountra, C., Bochkarev, A., Min, J., Ouyang, H.

To be published.

Macromolecule Content

Total Structure Weight: 33.86 kDa
Atom Count: 1,817
Modeled Residue Count: 229
Deposited Residue Count: 300
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromobox protein homolog 5	A, B, C, D	75	Homo sapiens	Mutation(s): 0 Gene Names: CBX5, HP1A
UniProt & NIH Common Fund Data Resources
Find proteins for P45973 (Homo sapiens) Explore P45973 Go to UniProtKB: P45973
PHAROS: P45973 GTEx: ENSG00000094916
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P45973
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 F [auth B] SDF format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.48 Å
R-Value Free: 0.303 (Depositor), 0.316 (DCC)
R-Value Work: 0.266 (Depositor), 0.282 (DCC)
R-Value Observed: 0.268 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.66	α = 90
b = 126.587	β = 90
c = 31.399	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-08-18

Deposition Author(s):

Kozieradzki, I.

Arrowsmith, C.H.

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2009-08-18
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2024-02-21
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.