6OXB | pdb_00006oxb

First bromo-adjacent homology (BAH) domain of human Polybromo-1 (PBRM1)

PDB DOI: https://doi.org/10.2210/pdb6OXB/pdb

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

Deposited: 2019-05-13 Released: 2020-05-20
Deposition Author(s): Petojevic, T., Holliday, M.J., Fairbrother, W.J., Cochran, A.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free:
0.217 (Depositor), 0.218 (DCC)
R-Value Work:
0.179 (Depositor), 0.179 (DCC)
R-Value Observed:
0.179 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6OXB

This is version 1.1 of the entry. See complete history.

Literature

Polyvalent nucleosome recognition by Polybromo-1 anchors chromatin remodeling

Petojevic, T., Holliday, M.J., Dimitrova, Y.N., Noland, C.L., Fairbrother, W.J., Cochran, A.G.

To be published.

Macromolecule Content

Total Structure Weight: 125.24 kDa
Atom Count: 8,790
Modeled Residue Count: 947
Deposited Residue Count: 1,062
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein polybromo-1	A [auth B] B [auth A] C D E A [auth B], B [auth A], C, D, E, F	177	Homo sapiens	Mutation(s): 0 Gene Names: PBRM1, BAF180, PB1
UniProt & NIH Common Fund Data Resources
Find proteins for Q86U86 (Homo sapiens) Explore Q86U86 Go to UniProtKB: Q86U86
PHAROS: Q86U86 GTEx: ENSG00000163939
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q86U86
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain Y [auth D] SDF format, chain X [auth D] SDF format, chain W [auth C] SDF format, chain V [auth C] SDF format, chain U [auth C] SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain KA [auth F] SDF format, chain K [auth B] SDF format, chain JA [auth F] SDF format, chain J [auth B] SDF format, chain IA [auth F] SDF format, chain I [auth B] SDF format, chain HA [auth F] SDF format, chain H [auth B] SDF format, chain GA [auth F] SDF format, chain G [auth B] SDF format, chain FA [auth E] SDF format, chain EA [auth E] SDF format, chain DA [auth E] SDF format, chain CA [auth E] SDF format, chain BA [auth E] SDF format, chain AA [auth D] MOL2 format, chain Z [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain X [auth D] MOL2 format, chain W [auth C] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain KA [auth F] MOL2 format, chain K [auth B] MOL2 format, chain JA [auth F] MOL2 format, chain J [auth B] MOL2 format, chain IA [auth F] MOL2 format, chain I [auth B] MOL2 format, chain HA [auth F] MOL2 format, chain H [auth B] MOL2 format, chain GA [auth F] MOL2 format, chain G [auth B] MOL2 format, chain FA [auth E] MOL2 format, chain EA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain CA [auth E] MOL2 format, chain BA [auth E] MOL2 format, chain AA [auth D] mmCIF format, chain Z [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain X [auth D] mmCIF format, chain W [auth C] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain KA [auth F] mmCIF format, chain K [auth B] mmCIF format, chain JA [auth F] mmCIF format, chain J [auth B] mmCIF format, chain IA [auth F] mmCIF format, chain I [auth B] mmCIF format, chain HA [auth F] mmCIF format, chain H [auth B] mmCIF format, chain GA [auth F] mmCIF format, chain G [auth B] mmCIF format, chain FA [auth E] mmCIF format, chain EA [auth E] mmCIF format, chain DA [auth E] mmCIF format, chain CA [auth E] mmCIF format, chain BA [auth E] mmCIF format, chain AA [auth D]	AA [auth D] BA [auth E] CA [auth E] DA [auth E] EA [auth E] AA [auth D], BA [auth E], CA [auth E], DA [auth E], EA [auth E], FA [auth E], G [auth B], GA [auth F], H [auth B], HA [auth F], I [auth B], IA [auth F], J [auth B], JA [auth F], K [auth B], KA [auth F], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], S [auth C], T [auth C], U [auth C], V [auth C], W [auth C], X [auth D], Y [auth D], Z [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth D] Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain G [auth B] Focus chain GA [auth F] Focus chain H [auth B] Focus chain HA [auth F] Focus chain I [auth B] Focus chain IA [auth F] Focus chain J [auth B] Focus chain JA [auth F] Focus chain K [auth B] Focus chain KA [auth F] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain G [auth B] Focus chain GA [auth F] Focus chain H [auth B] Focus chain HA [auth F] Focus chain I [auth B] Focus chain IA [auth F] Focus chain J [auth B] Focus chain JA [auth F] Focus chain K [auth B] Focus chain KA [auth F] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain R [auth A] SDF format, chain LA [auth F] MOL2 format, chain R [auth A] MOL2 format, chain LA [auth F] mmCIF format, chain R [auth A] mmCIF format, chain LA [auth F]	LA [auth F], R [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain LA [auth F] Focus chain R [auth A] Interactions & Density Focus chain LA [auth F] Focus chain R [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free: 0.217 (Depositor), 0.218 (DCC)
R-Value Work: 0.179 (Depositor), 0.179 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.304	α = 89.11
b = 52.255	β = 88.24
c = 120.1	γ = 60.12

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2020-05-20

Deposition Author(s):

Fairbrother, W.J.

Revision History (Full details and data files)

Version 1.0: 2020-05-20
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.