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- PDB-6xz5: RovC - regulator of virulence interconnected with the Csr system -

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Basic information

Entry
Database: PDB / ID: 6xz5
TitleRovC - regulator of virulence interconnected with the Csr system
ComponentsUncharacterized protein,RovC,Uncharacterized protein
KeywordsDNA BINDING PROTEIN / transcriptional activator / type VI secretion / hexameric ring / regulator of virulence
Function / homologyDomain of unknown function DUF2285 / T6SS, Transcription factor, DNA binding domain / Uncharacterized protein
Function and homology information
Biological speciesYersinia pseudotuberculosis serotype O:3
Yersinia pseudotuberculosis YPIII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsSadana, P. / Scrima, A.
CitationJournal: Plos Pathog. / Year: 2020
Title: RovC - a novel type of hexameric transcriptional activator promoting type VI secretion gene expression.
Authors: Knittel, V. / Sadana, P. / Seekircher, S. / Stolle, A.S. / Korner, B. / Volk, M. / Jeffries, C.M. / Svergun, D.I. / Heroven, A.K. / Scrima, A. / Dersch, P.
History
DepositionFeb 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein,RovC,Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6703
Polymers28,4781
Non-polymers1922
Water72140
1
A: Uncharacterized protein,RovC,Uncharacterized protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)172,01818
Polymers170,8666
Non-polymers1,15312
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5
Unit cell
Length a, b, c (Å)97.278, 97.278, 46.041
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-430-

HOH

21A-439-

HOH

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Components

#1: Protein Uncharacterized protein,RovC,Uncharacterized protein


Mass: 28477.619 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: An elongated stretch of ill-defined electron density is present, which corresponds to structural elements of the region 137-180. Individual amino acids could not be identified and the ...Details: An elongated stretch of ill-defined electron density is present, which corresponds to structural elements of the region 137-180. Individual amino acids could not be identified and the numbering has been assigned to 145-170 based on secondary structure prediction. Numbering in the region 145-170 may thus be not be accurate and residues are assigned as UNK.
Source: (gene. exp.) Yersinia pseudotuberculosis serotype O:3 (strain YPIII) (bacteria), (gene. exp.) Yersinia pseudotuberculosis YPIII (bacteria)
Gene: YPK_3567 / Cell line (production host): Rosetta2 (DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H3B5N9
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.21 Å3/Da / Density % sol: 44.3 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2 M KCl, 0.01 M MgSO4 , 0.01 M MES pH 5.6, 10% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.3→33.44 Å / Num. obs: 11309 / % possible obs: 99.5 % / Redundancy: 4 % / Biso Wilson estimate: 38.67 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.047 / Rrim(I) all: 0.096 / Net I/σ(I): 9.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.3-2.3840.566435610950.6940.3270.6572.399.9
8.91-33.443.80.027962100.9990.0110.02321.796.2

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Processing

Software
NameVersionClassification
Aimless0.5.29data scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→33.44 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 0.23 / Phase error: 27.34
RfactorNum. reflection% reflection
Rfree0.2739 558 4.96 %
Rwork0.2287 --
obs0.231 11306 96.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 100.79 Å2 / Biso mean: 49.8864 Å2 / Biso min: 22.45 Å2
Refinement stepCycle: final / Resolution: 2.3→33.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1682 0 10 40 1732
Biso mean--64.58 45.58 -
Num. residues----214
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021725
X-RAY DIFFRACTIONf_angle_d0.3722331
X-RAY DIFFRACTIONf_chiral_restr0.038250
X-RAY DIFFRACTIONf_plane_restr0.001294
X-RAY DIFFRACTIONf_dihedral_angle_d1.8131015
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3004-2.42170.31861490.2785284097
2.4217-2.57340.3441390.2761286698
2.5734-2.7720.32561590.2509271693
2.772-3.05080.25011350.2438291599
3.0508-3.49180.29281450.2265279896
3.4918-4.39770.2251470.192284997
4.3977-33.440.27741600.2313280895

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