3DB5

Crystal structure of methyltransferase domain of human PR domain-containing protein 4

• PDB DOI: https://doi.org/10.2210/pdb3DB5/pdb

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


• Deposited: 2008-05-30 Released: 2008-08-12 
• Deposition Author(s): Amaya, M.F., Zeng, H., 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: 2.15 Å
• R-Value Free: 
  0.298 (Depositor), 0.287 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Literature

The crystal structure of methyltransferase domain of human PR domain-containing protein 4.

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

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 35.05 kDa 
• Atom Count: 2,201 
• Modelled Residue Count: 258 
• Deposited Residue Count: 302 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PR domain zinc finger protein 4	A, B	151	Homo sapiens	Mutation(s): 0  Gene Names: PRDM4, PFM1 EC: 2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKN5 (Homo sapiens) Explore Q9UKN5  Go to UniProtKB:  Q9UKN5
PHAROS:  Q9UKN5 GTEx:  ENSG00000110851

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.298 (Depositor), 0.287 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.294	α = 90
b = 107.294	β = 90
c = 133.642	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-12 
Deposition Author(s): Amaya, M.F., Zeng, H., 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: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary