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- PDB-1z21: Crystal structure of the core domain of Yersinia pestis virulence... -

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Basic information

Entry
Database: PDB / ID: 1z21
TitleCrystal structure of the core domain of Yersinia pestis virulence factor YopR
ComponentsYop proteins translocation protein H
KeywordsCELL INVASION / Yersinia pestis / plague / type III secretion / YopR / yop
Function / homology
Function and homology information


type III protein secretion system complex / protein secretion by the type III secretion system / :
Similarity search - Function
Type III secretion system virulence factor YopR, core domain / Type III secretion system effector YopR / Type III secretion system virulence factor YopR, core domain / YopR, type III needle-polymerisation regulator / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Yop proteins translocation protein H
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.499 Å
AuthorsSchubot, F.D. / Cherry, S. / Tropea, J.E. / Austin, B.P. / Waugh, D.S.
CitationJournal: Protein Sci. / Year: 2005
Title: Crystal structure of the protease-resistant core domain of Yersinia pestis virulence factor YopR.
Authors: Schubot, F.D. / Cherry, S. / Austin, B.P. / Tropea, J.E. / Waugh, D.S.
History
DepositionMar 7, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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: Yop proteins translocation protein H


Theoretical massNumber of molelcules
Total (without water)12,6061
Polymers12,6061
Non-polymers00
Water2,126118
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.662, 85.662, 85.662
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11A-209-

HOH

21A-223-

HOH

31A-224-

HOH

41A-259-

HOH

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Components

#1: Protein Yop proteins translocation protein H / Low calcium response locus protein P


Mass: 12606.379 Da / Num. of mol.: 1 / Fragment: YopR(38-149)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: yscH, lcrP / Plasmid: pDEST-MBP / Production host: Escherichia coli (E. coli) / Strain (production host): BL31(DE3)CodonPlus-RIL / References: UniProt: P68590
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O

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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: 2.1 Å3/Da / Density % sol: 40.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 17% PEG-8000, 85 mM Phosphate-citrate, 0.17 M NaCl, and 15% glycerol, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1 Å
DetectorType: BRANDEIS / Detector: CCD / Date: Sep 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→22.82 Å / Num. all: 17699 / Num. obs: 17807 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.036 / Rsym value: 0.036 / Net I/σ(I): 46.1
Reflection shellResolution: 1.5→1.54 Å / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 1.499→22.81 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.544 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.112 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23833 640 5 %RANDOM
Rwork0.20357 ---
all0.2691 17807 --
obs0.20526 12054 71.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.596 Å2
Refinement stepCycle: LAST / Resolution: 1.499→22.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms771 0 0 118 889
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.021777
X-RAY DIFFRACTIONr_bond_other_d0.0020.02731
X-RAY DIFFRACTIONr_angle_refined_deg1.0191.9781052
X-RAY DIFFRACTIONr_angle_other_deg0.74331692
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.588594
X-RAY DIFFRACTIONr_chiral_restr0.0570.2123
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02840
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02145
X-RAY DIFFRACTIONr_nbd_refined0.250.2310
X-RAY DIFFRACTIONr_nbd_other0.2220.2857
X-RAY DIFFRACTIONr_nbtor_other0.0840.2430
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2160.221
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2770.251
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1770.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.21
X-RAY DIFFRACTIONr_mcbond_it0.6671.5479
X-RAY DIFFRACTIONr_mcangle_it1.2852770
X-RAY DIFFRACTIONr_scbond_it1.7623298
X-RAY DIFFRACTIONr_scangle_it3.0134.5282
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.29 19
Rwork0.405 327

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