2Y7I

Structural basis for high arginine specificity in Salmonella typhimurium periplasmic binding protein STM4351.

PDB DOI: https://doi.org/10.2210/pdb2Y7I/pdb

Classification: ARGININE-BINDING PROTEIN
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2011-01-31 Released: 2011-05-11
Deposition Author(s): Stamp, A.L., Owen, P., El Omari, K., Lockyer, M., Lamb, H.K., Charles, I.G., Hawkins, A.R., Stammers, D.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.226
R-Value Work: 0.198
R-Value Observed: 0.199

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystallographic and Microcalorimetric Analyses Reveal the Structural Basis for High Arginine Specificity in the Salmonella Enterica Serovar Typhimurium Periplasmic Binding Protein Stm4351.

Stamp, A.L., Owen, P., El Omari, K., Lockyer, M., Lamb, H.K., Charles, I.G., Hawkins, A.R., Stammers, D.K.

(2011) Proteins 79: 2352

PubMed: 21560168 Search on PubMed
DOI: https://doi.org/10.1002/prot.23060
Primary Citation of Related Structures:
2Y7I

Organizational Affiliation

Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom.

Macromolecule Content

Total Structure Weight: 52.19 kDa
Atom Count: 3,878
Modelled Residue Count: 452
Deposited Residue Count: 458
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
STM4351	A, B	229	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0
UniProt
Find proteins for Q8ZKA9 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q8ZKA9 Go to UniProtKB: Q8ZKA9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8ZKA9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ARG Query on ARG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain I [auth B]	C [auth A], I [auth B]	ARGININE C₆ H₁₅ N₄ O₂ ODKSFYDXXFIFQN-BYPYZUCNSA-O		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain M [auth B] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B]	H [auth A], M [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain M [auth B] Interactions & Density Focus chain H [auth A] Focus chain M [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain F [auth A] SDF format, chain N [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain F [auth A] MOL2 format, chain N [auth B]	D [auth A] E [auth A] F [auth A] J [auth B] K [auth B] D [auth A], E [auth A], F [auth A], J [auth B], K [auth B], N [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain G [auth A]	G [auth A], L [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain L [auth B] Interactions & Density Focus chain G [auth A] Focus chain L [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
ARG	PDBBind: 2Y7I	Kd: 2900 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.226
R-Value Work: 0.198
R-Value Observed: 0.199
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.317	α = 90
b = 56.331	β = 100.17
c = 88.37	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-05-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-05-11
Type: Initial release
Version 1.1: 2011-06-16
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description

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Help and Resources

2Y7I

Structural basis for high arginine specificity in Salmonella typhimurium periplasmic binding protein STM4351.

Crystallographic and Microcalorimetric Analyses Reveal the Structural Basis for High Arginine Specificity in the Salmonella Enterica Serovar Typhimurium Periplasmic Binding Protein Stm4351.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)