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- PDB-7z06: Structure of YwlG (Q2FF14) from Staphylococcus aureus -

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Basic information

Entry
Database: PDB / ID: 7z06
TitleStructure of YwlG (Q2FF14) from Staphylococcus aureus
ComponentsUPF0340 protein SAUSA300_2068
KeywordsUNKNOWN FUNCTION / hexameric complex
Function / homologyProtein of unknown function DUF436 / Protein of unknown function (DUF436) / Aminoglycoside 3-N-acetyltransferase-like / UPF0340 protein SAUSA300_2068
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.74 Å
AuthorsSchneider, S. / Scheidler, C.M. / Sieber, S.A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Bidirectional sequestration between a bacterial hibernation factor and a glutamate metabolizing protein.
Authors: Ranava, D. / Scheidler, C.M. / Pfanzelt, M. / Fiedler, M. / Sieber, S.A. / Schneider, S. / Yap, M.F.
History
DepositionFeb 22, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UPF0340 protein SAUSA300_2068
B: UPF0340 protein SAUSA300_2068
C: UPF0340 protein SAUSA300_2068
D: UPF0340 protein SAUSA300_2068
E: UPF0340 protein SAUSA300_2068
F: UPF0340 protein SAUSA300_2068
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,68923
Polymers128,0566
Non-polymers1,63317
Water7,224401
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.741, 136.878, 79.190
Angle α, β, γ (deg.)90.00, 98.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
UPF0340 protein SAUSA300_2068


Mass: 21342.684 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: USA300 / Gene: SAUSA300_2068 / Production host: Escherichia coli B (bacteria) / Strain (production host): BL21 / References: UniProt: Q2FF14
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.1 M BICINE 1.6 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.74→47.99 Å / Num. obs: 114645 / % possible obs: 97.8 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 10.42
Reflection shellResolution: 1.74→1.81 Å / Redundancy: 3.1 % / Num. unique obs: 10476 / CC1/2: 0.516 / % possible all: 88.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VD8

1vd8


Resolution: 1.74→47.99 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.275 5721 -
Rwork0.25 --
obs-114504 97.8 %
Displacement parametersBiso mean: 18.87 Å2
Refinement stepCycle: LAST / Resolution: 1.74→47.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8025 0 85 401 8511
LS refinement shellResolution: 1.74→1.81 Å
RfactorNum. reflection% reflection
Rfree0.456 515 5 %
Rwork0.448 10390 -
obs--88.8 %

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