6NB0 | pdb_00006nb0

Crystal structure of Histidine kinase from Burkholderia phymatum STM815

PDB DOI: https://doi.org/10.2210/pdb6NB0/pdb

Classification: TRANSFERASE
Organism(s): Paraburkholderia phymatum STM815
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2018-12-06 Released: 2018-12-19
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.222 (Depositor), 0.222 (DCC)
R-Value Work:
0.191 (Depositor), 0.193 (DCC)
R-Value Observed:
0.193 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 6NB0

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

Literature

Crystal structure of Histidine kinase from Burkholderia phymatum STM815

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

To be published.

Macromolecule Content

Total Structure Weight: 31.02 kDa
Atom Count: 1,859
Modeled Residue Count: 219
Deposited Residue Count: 287
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histidine kinase	A	287	Paraburkholderia phymatum STM815	Mutation(s): 0 Gene Names: Bphy_4385 EC: 2.7.13.3
UniProt
Find proteins for B2JQF9 (Paraburkholderia phymatum (strain DSM 17167 / CIP 108236 / LMG 21445 / STM815)) Explore B2JQF9 Go to UniProtKB: B2JQF9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B2JQF9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.222 (Depositor), 0.222 (DCC)
R-Value Work: 0.191 (Depositor), 0.193 (DCC)
R-Value Observed: 0.193 (Depositor)

Diffraction Data:

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.6	α = 90
b = 77.6	β = 90
c = 97.17	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
PARROT	phasing
ARP/wARP	model building
Coot	model building

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2018-12-19

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2018-12-19
Type: Initial release
Version 1.1: 2024-03-13
Changes: Data collection, Database references

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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.