6PNV | pdb_00006pnv

1.42 Angstrom Resolution Crystal Structure of Translocation Protein TolB from Salmonella enterica

PDB DOI: https://doi.org/10.2210/pdb6PNV/pdb

Classification: TRANSLOCASE
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2-4
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-07-03 Released: 2019-07-17
Deposition Author(s): Minasov, G., Shuvalova, L., Dubrovska, I., Kiryukhina, O., Endres, M., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.42 Å
R-Value Free:
0.194 (Depositor), 0.204 (DCC)
R-Value Work:
0.162 (Depositor), 0.171 (DCC)
R-Value Observed:
0.164 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

1.42 Angstrom Resolution Crystal Structure of Translocation Protein TolB from Salmonella enterica

Minasov, G., Shuvalova, L., Dubrovska, I., Kiryukhina, O., Endres, M., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 44.03 kDa
Atom Count: 3,717
Modeled Residue Count: 411
Deposited Residue Count: 411
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tol-Pal system protein TolB	A	411	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2-4	Mutation(s): 0
UniProt
Find proteins for Q8ZQT5 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q8ZQT5 Go to UniProtKB: Q8ZQT5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8ZQT5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
K Query on K 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]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.42 Å
R-Value Free: 0.194 (Depositor), 0.204 (DCC)
R-Value Work: 0.162 (Depositor), 0.171 (DCC)
R-Value Observed: 0.164 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.894	α = 90
b = 40.57	β = 111.61
c = 77.994	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2019-07-17

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: 2019-07-17
Type: Initial release
Version 1.1: 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.