4IEJ | pdb_00004iej

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 (Depositor), 0.237 (DCC)
R-Value Work:
0.197 (Depositor)
R-Value Observed:
0.198 (Depositor)

Starting Model: experimental
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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
Modeled Residue Count: 75
Deposited Residue Count: 93
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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] mmCIF 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 (Depositor), 0.237 (DCC)
R-Value Work: 0.197 (Depositor)
R-Value Observed: 0.198 (Depositor)

Diffraction Data:

Space Group: P 6₁ 2 2

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

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View more in-depth experimental data

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

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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.