6SWL | pdb_00006swl

The REC domain of XynC, a response regulator from Geobacillus stearothermophilus

PDB DOI: https://doi.org/10.2210/pdb6SWL/pdb

Classification: TRANSCRIPTION
Organism(s): Geobacillus stearothermophilus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-09-22 Released: 2020-10-14
Deposition Author(s): Lansky, S., Lavid, N., Shoham, Y., Shoham, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.17 Å
R-Value Free:
0.257 (Depositor), 0.258 (DCC)
R-Value Work:
0.193 (Depositor), 0.204 (DCC)
R-Value Observed:
0.198 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

The REC domain of XynC, a response regulator from Geobacillus stearothermophilus

Lansky, S., Lavid, N., Shoham, Y., Shoham, G.

To be published.

Macromolecule Content

Total Structure Weight: 30.81 kDa
Atom Count: 2,147
Modeled Residue Count: 263
Deposited Residue Count: 266
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Two-component response regulator	A, B	133	Geobacillus stearothermophilus	Mutation(s): 0 Gene Names: xynC
UniProt
Find proteins for Q09LZ6 (Geobacillus stearothermophilus) Explore Q09LZ6 Go to UniProtKB: Q09LZ6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q09LZ6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PHD Query on PHD	A, B	L-PEPTIDE LINKING	C₄ H₈ N O₇ P		ASP

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.17 Å
R-Value Free: 0.257 (Depositor), 0.258 (DCC)
R-Value Work: 0.193 (Depositor), 0.204 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.3	α = 90
b = 130.3	β = 90
c = 40.51	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2020-10-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-10-14
Type: Initial release
Version 1.1: 2024-01-24
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.