4IEJ

Crystal structure of a DNA methyltransferase 1 associated protein 1 (DMAP1) from Homo sapiens at 1.45 A resolution

PDB DOI: https://doi.org/10.2210/pdb4IEJ/pdb

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

Deposited: 2012-12-13 Released: 2013-01-02
Deposition Author(s): Joint Center for Structural Genomics (JCSG), Partnership for T-Cell Biology (TCELL)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.226
R-Value Work: 0.197
R-Value Observed: 0.198

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of a DNA methyltransferase 1 associated protein 1 (DMAP1) from Homo sapiens at 1.45 A resolution

Joint Center for Structural Genomics (JCSG), Partnership for T-Cell Biology

To be published.

Macromolecule Content

Total Structure Weight: 11.26 kDa
Atom Count: 795
Modelled Residue Count: 75
Deposited Residue Count: 93
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA methyltransferase 1-associated protein 1	A	93	Homo sapiens	Mutation(s): 0 Gene Names: BC008053, DMAP1, KIAA1425
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NPF5 (Homo sapiens) Explore Q9NPF5 Go to UniProtKB: Q9NPF5
PHAROS: Q9NPF5 GTEx: ENSG00000178028
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NPF5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-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: 1.45 Å
R-Value Free: 0.226
R-Value Work: 0.197
R-Value Observed: 0.198
Space Group: P 6₁ 2 2
Diffraction Data: https://doi.org/10.18430/M34IEJ

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.353	α = 90
b = 37.353	β = 90
c = 229.96	γ = 120

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
MOLREP	phasing
XSCALE	data scaling
BUSTER-TNT	refinement
XDS	data reduction
BUSTER	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-01-02

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Partnership for T-Cell Biology (TCELL)

Revision History (Full details and data files)

Version 1.0: 2013-01-02
Type: Initial release
Version 1.1: 2013-01-09
Changes: Structure summary
Version 1.2: 2013-01-16
Changes: Structure summary
Version 1.3: 2017-11-15
Changes: Refinement description
Version 1.4: 2023-02-01
Changes: Database references, Derived calculations
Version 1.5: 2023-09-20
Changes: Data collection, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.