4EQ9 | pdb_00004eq9

1.4 Angstrom Crystal Structure of ABC Transporter Glutathione-Binding Protein GshT from Streptococcus pneumoniae strain Canada MDR_19A in Complex with Glutathione

PDB DOI: https://doi.org/10.2210/pdb4EQ9/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Streptococcus pneumoniae str. Canada MDR_19A
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-04-18 Released: 2012-05-02
Deposition Author(s): Minasov, G., Wawrzak, Z., Stogios, P.J., Light, S.H., Kudritska, M., Yim, V., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.190 (Depositor), 0.191 (DCC)
R-Value Work:
0.168 (Depositor), 0.175 (DCC)
R-Value Observed:
0.169 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

1.4 Angstrom Crystal Structure of Putative ABC Transporter Substrate-Binding Protein from Streptococcus pneumoniae strain Canada MDR_19A in Complex with Glutathione.

Minasov, G., Wawrzak, Z., Stogios, P.J., Light, S.H., Kudritska, M., Yim, V., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 28.04 kDa
Atom Count: 2,455
Modeled Residue Count: 240
Deposited Residue Count: 246
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC transporter substrate-binding protein-amino acid transport	A	246	Streptococcus pneumoniae str. Canada MDR_19A	Mutation(s): 0 Gene Names: ABC-SBP, spr0146
UniProt
Find proteins for Q8DRG2 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6)) Explore Q8DRG2 Go to UniProtKB: Q8DRG2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8DRG2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GSH Query on GSH 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]	Glutathione C₁₀ H₁₇ N₃ O₆ S RWSXRVCMGQZWBV-WDSKDSINSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002593 (GSH) Query on PRD_002593	B [auth A]	Glutathione	Peptide-like / Oxidation-reduction		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.190 (Depositor), 0.191 (DCC)
R-Value Work: 0.168 (Depositor), 0.175 (DCC)
R-Value Observed: 0.169 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.801	α = 90
b = 42.391	β = 94.7
c = 74.248	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-05-02

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2012-05-02
Type: Initial release
Version 1.1: 2013-04-24
Changes: Structure summary
Version 1.2: 2017-11-15
Changes: Refinement description
Version 1.3: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description