4ZEY | pdb_00004zey

Crystal structure of a nuclear receptor binding factor 2 MIT domain (NRBF2) from Homo sapiens at 1.50 A resolution

• PDB DOI: https://doi.org/10.2210/pdb4ZEY/pdb

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


• Deposited: 2015-04-20 Released: 2015-05-06 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG), Partnership for Nuclear Receptor Signaling Code Biology (NHRS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.248 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Literature

Crystal structure of a nuclear receptor binding factor 2 MIT domain (NRBF2) from Homo sapiens at 1.50 A resolution

Joint Center for Structural Genomics (JCSG), Partnership for Nuclear Receptor Signaling Code Biology (NHRs)

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 10.05 kDa 
• Atom Count: 797 
• Modeled Residue Count: 84 
• Deposited Residue Count: 84 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor-binding factor 2	A	84	Homo sapiens	Mutation(s): 0  Gene Names: NRBF2, COPR
UniProt & NIH Common Fund Data Resources
Find proteins for Q96F24 (Homo sapiens) Explore Q96F24  Go to UniProtKB:  Q96F24
PHAROS:  Q96F24 GTEx:  ENSG00000148572

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.248 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M3530H

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.48	α = 90
b = 34.05	β = 108.47
c = 52.34	γ = 90

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
SOLVE	phasing
XSCALE	data scaling
BUSTER-TNT	refinement
BUSTER	refinement
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-05-06 
Deposition Author(s): Joint Center for Structural Genomics (JCSG), Partnership for Nuclear Receptor Signaling Code Biology (NHRS)

Revision History  

• Version 1.0: 2015-05-06
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Derived calculations, Refinement description, Source and taxonomy, Structure summary
• Version 1.2: 2018-01-24
  Changes: Database references
• Version 1.3: 2023-02-01
  Changes: Database references
• Version 1.4: 2024-11-13
  Changes: Data collection, Structure summary