3DAL | pdb_00003dal

Methyltransferase domain of human PR domain-containing protein 1

• PDB DOI: https://doi.org/10.2210/pdb3DAL/pdb

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


• Deposited: 2008-05-29 Released: 2008-08-12 
• Deposition Author(s): Amaya, M.F., Zeng, H., Antoshenko, T., Dong, A., Loppnau, P., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Min, J., Plotnikov, A.N., Wu, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.217 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Literature

The crystal structure of methyltransferase domain of human PR domain-containing protein 1

Zeng, H., Amaya, M.F., Antoshenko, T., Dong, A., Loppnau, P., Bochkarev, A., Min, J., Plotnikov, A.N., Wu, H.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 45.38 kDa 
• Atom Count: 3,199 
• Modeled Residue Count: 345 
• Deposited Residue Count: 392 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PR domain zinc finger protein 1	A, B	196	Homo sapiens	Mutation(s): 0  Gene Names: PRDM1, BLIMP1 EC: 2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for O75626 (Homo sapiens) Explore O75626  Go to UniProtKB:  O75626
PHAROS:  O75626 GTEx:  ENSG00000057657

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.217 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.834	α = 90
b = 64.96	β = 90
c = 112.663	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-12 
Deposition Author(s): Amaya, M.F., Zeng, H., Antoshenko, T., Dong, A., Loppnau, P., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Min, J., Plotnikov, A.N., Wu, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2008-08-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references