4GNR

1.0 Angstrom resolution crystal structure of the branched-chain amino acid transporter substrate binding protein LivJ from Streptococcus pneumoniae str. Canada MDR_19A in complex with Isoleucine

PDB DOI: https://doi.org/10.2210/pdb4GNR/pdb

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

Deposited: 2012-08-17 Released: 2012-09-05
Deposition Author(s): Halavaty, A.S., Kudritska, M., Wawrzak, Z., Stogios, P.J., Yim, V., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.00 Å
R-Value Free: 0.147
R-Value Work: 0.126
R-Value Observed: 0.127

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

1.0 Angstrom resolution crystal structure of the branched-chain amino acid transporter substrate binding protein LivJ from Streptococcus pneumoniae str. Canada MDR_19A in complex with Isoleucine

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

To be published.

Macromolecule Content

Total Structure Weight: 37.46 kDa
Atom Count: 3,601
Modelled Residue Count: 348
Deposited Residue Count: 353
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC transporter substrate-binding protein-branched chain amino acid transport	A	353	Streptococcus pneumoniae str. Canada MDR_19A	Mutation(s): 0
UniProt
Find proteins for J9PBT7 (Streptococcus pneumoniae str. Canada MDR_19A) Explore J9PBT7 Go to UniProtKB: J9PBT7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	J9PBT7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ILE Query on ILE 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]	ISOLEUCINE C₆ H₁₃ N O₂ AGPKZVBTJJNPAG-WHFBIAKZSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	F [auth A], G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	C [auth A], D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY Query on MLY	A	L-PEPTIDE LINKING	C₈ H₁₈ N₂ O₂		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.00 Å
R-Value Free: 0.147
R-Value Work: 0.126
R-Value Observed: 0.127
Space Group: P 1 2₁ 1
Diffraction Data: https://doi.org/10.18430/m34gnr

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.274	α = 90
b = 72.819	β = 105.1
c = 57.542	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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Entry History

Deposition Data

Released Date: 2012-09-05

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2012-09-05
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

4GNR

1.0 Angstrom resolution crystal structure of the branched-chain amino acid transporter substrate binding protein LivJ from Streptococcus pneumoniae str. Canada MDR_19A in complex with Isoleucine

1.0 Angstrom resolution crystal structure of the branched-chain amino acid transporter substrate binding protein LivJ from Streptococcus pneumoniae str. Canada MDR_19A in complex with Isoleucine

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)