3G0J | pdb_00003g0j

Crystal Structure of the fifth Bromodomain of Human Poly-bromodomain containing protein 1 (PB1)

• PDB DOI: https://doi.org/10.2210/pdb3G0J/pdb

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


• Deposited: 2009-01-28 Released: 2009-02-10 
• Deposition Author(s): Filippakopoulos, P., Keates, T., Picaud, S., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 
  0.237 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Models: experimental

Literature

Crystal Structure of the fifth Bromodomain of Human Poly-bromodomain containing protein 1 (PB1)

Filippakopoulos, P., Keates, T., Picaud, S., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., 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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 29.61 kDa 
• Atom Count: 2,181 
• Modeled Residue Count: 228 
• Deposited Residue Count: 248 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein polybromo-1	A, B	124	Homo sapiens	Mutation(s): 0  Gene Names: PBRM1
UniProt & NIH Common Fund Data Resources
Find proteins for Q86U86 (Homo sapiens) Explore Q86U86  Go to UniProtKB:  Q86U86
PHAROS:  Q86U86 GTEx:  ENSG00000163939

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free:  0.237 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.57	α = 90
b = 57.37	β = 90
c = 137.3	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-02-10 
Deposition Author(s): Filippakopoulos, P., Keates, T., Picaud, S., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2009-02-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description