3RAY | pdb_00003ray

Crystal structure of Methyltransferase domain of human PR domain-containing protein 11

• PDB DOI: https://doi.org/10.2210/pdb3RAY/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-03-28 Released: 2011-04-20 
• Deposition Author(s): Dong, A., Zeng, H., Loppnau, P., Walker, J.R., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Min, J., Wu, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 
  0.228 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Methyltransferase domain of human PR domain-containing protein 11

Dong, A., Zeng, H., Loppnau, P., Walker, J.R., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Min, J., Wu, H., Structural Genomics Consortium (SGC)

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 27.62 kDa 
• Atom Count: 1,446 
• Modeled Residue Count: 159 
• Deposited Residue Count: 237 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PR domain-containing protein 11	A	237	Homo sapiens	Mutation(s): 0  Gene Names: PRDM11, PFM8 EC: 2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NQV5 (Homo sapiens) Explore Q9NQV5  Go to UniProtKB:  Q9NQV5
PHAROS:  Q9NQV5 GTEx:  ENSG00000019485

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	D [auth A], E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N
UNX	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free:  0.228 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.154	α = 90
b = 55.156	β = 90
c = 106.283	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
PHASES	phasing
BUSTER	refinement
Coot	model building
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-20 
Deposition Author(s): Dong, A., Zeng, H., Loppnau, P., Walker, J.R., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Min, J., Wu, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2011-04-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description