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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.226 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

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

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.226 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34IEJ

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

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  

• 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