4LC2 | pdb_00004lc2

Crystal structure of the bromodomain of human BRPF1B

• PDB DOI: https://doi.org/10.2210/pdb4LC2/pdb

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


• Deposited: 2013-06-21 Released: 2013-07-24 
• Deposition Author(s): Tallant, C., Nunez-Alonso, G., Savitsky, P., Picaud, S., Filippakopoulos, P., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.220 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Models: experimental

Literature

Crystal structure of the bromodomain of human BRPF1B

Tallant, C., Nunez-Alonso, G., Savitsky, P., Picaud, S., Filippakopoulos, P., von Delft, F., Arrowsmith, H.C., Edwards, M.A., Bountra, C., Knapp, S.

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: 13.83 kDa 
• Atom Count: 1,091 
• Modeled Residue Count: 114 
• Deposited Residue Count: 116 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peregrin	A	116	Homo sapiens	Mutation(s): 0  Gene Names: BR140, BRPF1, BRPF1B
UniProt & NIH Common Fund Data Resources
Find proteins for P55201 (Homo sapiens) Explore P55201  Go to UniProtKB:  P55201
PHAROS:  P55201 GTEx:  ENSG00000156983

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NO3	B [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.220 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.835	α = 90
b = 60.835	β = 90
c = 63.679	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-24 
Deposition Author(s): Tallant, C., Nunez-Alonso, G., Savitsky, P., Picaud, S., Filippakopoulos, P., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2013-07-24
  Type: Initial release
  
• Version 1.1: 2018-01-31
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description