4MN5 | pdb_00004mn5

Crystal structure of PAS domain of S. aureus YycG

PDB DOI: https://doi.org/10.2210/pdb4MN5/pdb

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

Deposited: 2013-09-10 Released: 2014-09-10
Deposition Author(s): Shaikh, N., Hvorup, R., Winnen, B., Collins, B.M., King, G.F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.253 (Depositor), 0.254 (DCC)
R-Value Work:
0.221 (Depositor), 0.215 (DCC)
R-Value Observed:
0.222 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4MN5

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

Literature

Crystal structure of PAS domain of S. aureus YycG

Shaikh, N., Hvorup, R., Winnen, B., Collins, B.M., King, G.F.

To be published.

Macromolecule Content

Total Structure Weight: 29.79 kDa
Atom Count: 1,707
Modeled Residue Count: 204
Deposited Residue Count: 256
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sensor protein kinase WalK	A, B	128	Staphylococcus aureus	Mutation(s): 0 Gene Names: vicK, walK, yycG EC: 2.7.13.3
UniProt
Find proteins for Q9RDT3 (Staphylococcus aureus) Explore Q9RDT3 Go to UniProtKB: Q9RDT3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9RDT3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.253 (Depositor), 0.254 (DCC)
R-Value Work: 0.221 (Depositor), 0.215 (DCC)
R-Value Observed: 0.222 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.82	α = 90
b = 60.51	β = 90
c = 84.5	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
SOLVE	phasing
PHENIX	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-09-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-09-10
Type: Initial release
Version 1.1: 2024-11-27
Changes: Data collection, Database references, Derived calculations, Structure summary

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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.