4XLT | pdb_00004xlt

Crystal structure of response regulator receiver protein from Dyadobacter fermentans DSM 18053

PDB DOI: https://doi.org/10.2210/pdb4XLT/pdb

Classification: SIGNALING PROTEIN
Organism(s): Dyadobacter fermentans DSM 18053
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2015-01-13 Released: 2015-01-28
Deposition Author(s): Chang, C., Cuff, M., Holowicki, J., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.249 (Depositor), 0.254 (DCC)
R-Value Work:
0.193 (Depositor), 0.201 (DCC)
R-Value Observed:
0.196 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of response regulator receiver protein from Dyadobacter fermentans DSM 18053

Chang, C., Cuff, M., Holowicki, J., Clancy, S., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 15.19 kDa
Atom Count: 1,069
Modeled Residue Count: 128
Deposited Residue Count: 133
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Response regulator receiver protein	A	133	Dyadobacter fermentans DSM 18053	Mutation(s): 0 Gene Names: Dfer_0154
UniProt
Find proteins for C6VVW9 (Dyadobacter fermentans (strain ATCC 700827 / DSM 18053 / CIP 107007 / KCTC 52180 / NS114)) Explore C6VVW9 Go to UniProtKB: C6VVW9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C6VVW9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.249 (Depositor), 0.254 (DCC)
R-Value Work: 0.193 (Depositor), 0.201 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.945	α = 90
b = 62.945	β = 90
c = 69.486	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
Coot	model building
HKL-3000	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-01-28

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2015-01-28
Type: Initial release
Version 1.1: 2024-10-23
Changes: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary

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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.