1GV5 | pdb_00001gv5

CRYSTAL STRUCTURE OF C-MYB R2

PDB DOI: https://doi.org/10.2210/pdb1GV5/pdb

Classification: TRANSCRIPTION
Organism(s): Mus musculus
Mutation(s): Yes

Deposited: 2002-02-06 Released: 2003-07-03
Deposition Author(s): Tahirov, T.H., Ogata, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.58 Å
R-Value Free:
0.190 (Depositor)
R-Value Work:
0.178 (Depositor), 0.172 (DCC)
R-Value Observed:
0.178 (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 C-Myb DNA-Binding Domain: Specific Na+ Binding and Correlation with NMR Structure

Tahirov, T.H., Morii, H., Uedaira, H., Sasaki, M., Sarai, A., Adachi, S., Park, S.Y., Kamiya, N., Ogata, K.

To be published.

Macromolecule Content

Total Structure Weight: 6.33 kDa
Atom Count: 526
Modeled Residue Count: 52
Deposited Residue Count: 52
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MYB PROTO-ONCOGENE PROTEIN	A	52	Mus musculus	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for P06876 (Mus musculus) Explore P06876 Go to UniProtKB: P06876
IMPC: MGI:97249
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P06876
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: 1.58 Å
R-Value Free: 0.190 (Depositor)
R-Value Work: 0.178 (Depositor), 0.172 (DCC)
R-Value Observed: 0.178 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 28.832	α = 90
b = 40.182	β = 90
c = 49.229	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2003-07-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2003-07-03
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2019-05-08
Changes: Data collection, Experimental preparation, Other
Version 1.4: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, 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.