4GT8 | pdb_00004gt8

Crystal Structure of the Catalytic and ATP-binding Domain from VraS in Complex with ADP

PDB DOI: https://doi.org/10.2210/pdb4GT8/pdb

Classification: TRANSFERASE
Organism(s): Staphylococcus aureus subsp. aureus Mu50
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-08-28 Released: 2013-08-28
Deposition Author(s): Leonard, P.G., Valverde, J., Stock, A.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.51 Å
R-Value Free:
0.199 (Depositor), 0.200 (DCC)
R-Value Work:
0.183 (Depositor), 0.180 (DCC)
R-Value Observed:
0.184 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of the Staphylococcus aureus VraS Catalytic and ATP-binding Domain

Leonard, P.G., Valverde, J., Stock, A.M.

To be published.

Macromolecule Content

Total Structure Weight: 16.23 kDa
Atom Count: 1,246
Modeled Residue Count: 133
Deposited Residue Count: 139
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sensor protein vraS	A	139	Staphylococcus aureus subsp. aureus Mu50	Mutation(s): 0 Gene Names: SAV1885, vraS EC: 2.7.13.3
UniProt
Find proteins for Q7A2Q0 (Staphylococcus aureus (strain Mu50 / ATCC 700699)) Explore Q7A2Q0 Go to UniProtKB: Q7A2Q0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7A2Q0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP 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]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MG Query on MG 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]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-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: 1.51 Å
R-Value Free: 0.199 (Depositor), 0.200 (DCC)
R-Value Work: 0.183 (Depositor), 0.180 (DCC)
R-Value Observed: 0.184 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.192	α = 90
b = 47.233	β = 90
c = 89.398	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
RESOLVE	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-08-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-08-28
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations

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.