6DB1 | pdb_00006db1

2.0 Angstrom Resolution Crystal Structure of N-Terminal Ligand-Binding Domain of Putative Methyl-Accepting Chemotaxis Protein from Salmonella enterica

PDB DOI: https://doi.org/10.2210/pdb6DB1/pdb

Classification: TRANSFERASE
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-05-02 Released: 2018-05-16
Deposition Author(s): Minasov, G., Shuvalova, L., Dubrovska, I., Kiryukhina, O., Grimshaw, S., Kwon, K., Anderson, W.F., Satchell, K.J.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.264 (Depositor), 0.277 (DCC)
R-Value Work:
0.222 (Depositor), 0.236 (DCC)
R-Value Observed:
0.224 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

2.0 Angstrom Resolution Crystal Structure of N-Terminal Ligand-Binding Domain of Putative Methyl-Accepting Chemotaxis Protein from Salmonella enterica.

Minasov, G., Shuvalova, L., Dubrovska, I., Kiryukhina, O., Grimshaw, S., Kwon, K., Anderson, W.F., Satchell, K.J.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 35.7 kDa
Atom Count: 2,288
Modeled Residue Count: 272
Deposited Residue Count: 316
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative methyl-accepting chemotaxis protein	A, B	158	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0 Gene Names: STM3152
UniProt
Find proteins for Q8ZM14 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q8ZM14 Go to UniProtKB: Q8ZM14
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8ZM14
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.264 (Depositor), 0.277 (DCC)
R-Value Work: 0.222 (Depositor), 0.236 (DCC)
R-Value Observed: 0.224 (Depositor)

Diffraction Data:

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.226	α = 90
b = 89.226	β = 90
c = 65.89	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2018-05-16

Deposition Author(s):

Satchell, K.J.F.

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2018-05-16
Type: Initial release
Version 1.1: 2024-11-06
Changes: Data collection, Database references, 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.