6N2L | pdb_00006n2l

Crystal structure of a histone family protein DNA-binding protein from Burkholderia ambifaria

PDB DOI: https://doi.org/10.2210/pdb6N2L/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Burkholderia ambifaria MC40-6
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2018-11-13 Released: 2018-12-05
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.295 (Depositor), 0.300 (DCC)
R-Value Work:
0.245 (Depositor), 0.249 (DCC)
R-Value Observed:
0.249 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of a histone family protein DNA-binding protein from Burkholderia ambifaria

Abendroth, J., Mayclin, S.J., Lorimer, D., Horanyi, P.S., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 10.65 kDa
Atom Count: 672
Modeled Residue Count: 88
Deposited Residue Count: 100
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone family protein DNA-binding protein	A	100	Burkholderia ambifaria MC40-6	Mutation(s): 0 Gene Names: BamMC406_0065
UniProt
Find proteins for B1YQ53 (Burkholderia ambifaria (strain MC40-6)) Explore B1YQ53 Go to UniProtKB: B1YQ53
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B1YQ53
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.295 (Depositor), 0.300 (DCC)
R-Value Work: 0.245 (Depositor), 0.249 (DCC)
R-Value Observed: 0.249 (Depositor)

Diffraction Data:

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.21	α = 90
b = 71.4	β = 90
c = 76.73	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MoRDa	phasing
Coot	model building

Structure Validation

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Entry History

Deposition Data

Released Date: 2018-12-05

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2018-12-05
Type: Initial release
Version 1.1: 2018-12-19
Changes: Data collection, Refinement description
Version 1.2: 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.