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- PDB-4jbu: 1.65A structure of the T3SS tip protein LcrV (G28-D322, C273S) fr... -

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Basic information

Entry
Database: PDB / ID: 4jbu
Title1.65A structure of the T3SS tip protein LcrV (G28-D322, C273S) from Yersinia pestis
ComponentsVirulence-associated V antigen
KeywordsPROTEIN BINDING / LcrV / T3SS / tip protein / Yersinia pestis
Function / homologyLow calcium response V antigen / Virulence-associated V antigen superfamily / V antigen (LcrV) protein / extracellular region / Virulence-associated V antigen
Function and homology information
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsLovell, S. / Chaudhury, S. / Battaile, K.P. / Plano, G. / De Guzman, R.N.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Structure of the Yersinia pestis tip protein LcrV refined to 1.65A resolution
Authors: Chaudhury, S. / Battaile, K.P. / Lovell, S. / Plano, G.V. / De Guzman, R.N.
History
DepositionFeb 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Virulence-associated V antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1542
Polymers33,9591
Non-polymers1941
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.553, 51.442, 65.178
Angle α, β, γ (deg.)90.000, 92.000, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Virulence-associated V antigen / Low calcium response locus protein V


Mass: 33959.305 Da / Num. of mol.: 1 / Fragment: UNP residues 28-322 / Mutation: C273S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Plasmid: pGEV2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) DNAY / References: UniProt: P0C7U7
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 1.95 Å3/Da / Density % sol: 36.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 25% (w/v) PEG 3350, 100 mM Bicine, pH 7.0, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→51.44 Å / Num. all: 31392 / Num. obs: 31392 / % possible obs: 99.32 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.29 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 17.9825
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
1.65-1.743.270.52.214857454699.84
1.74-1.843.320.313.614535438299.93
1.84-1.973.440.186.214037408099.86
1.97-2.133.350.1110.212619376499.7
2.13-2.333.240.0715.711411352699.74
2.33-2.613.430.0422.310828315399.58
2.61-3.013.170.0329.78773277198.74
3.01-3.693.090.0243.87254234798.23
3.69-5.223.270.02595919181097.78
5.22-51.443.130.0156.83174101395.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å34.33 Å
Translation2.5 Å34.33 Å

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Processing

Software
NameVersionClassificationNB
SCALACCP4_3.3.16data scaling
PHASER2.3.0phasing
PHENIXdev_961refinement
PDB_EXTRACT3.11data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1R6F

1r6f


Resolution: 1.65→34.33 Å / Occupancy max: 1 / Occupancy min: 0.33 / SU ML: 0.24 / σ(F): 0 / Phase error: 20.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2202 1582 5.04 %RANDOM
Rwork0.1774 ---
obs0.1795 31372 99.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.626 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso max: 77.22 Å2 / Biso mean: 28.5916 Å2 / Biso min: 11.67 Å2
Baniso -1Baniso -2Baniso -3
1-1.0556 Å20 Å23.648 Å2
2--2.7629 Å2-0 Å2
3----3.8186 Å2
Refinement stepCycle: LAST / Resolution: 1.65→34.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2186 0 10 149 2345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112261
X-RAY DIFFRACTIONf_angle_d1.1963051
X-RAY DIFFRACTIONf_chiral_restr0.069351
X-RAY DIFFRACTIONf_plane_restr0.006392
X-RAY DIFFRACTIONf_dihedral_angle_d13.477870
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
1.65-1.70330.33841420.2733267728192677100
1.7033-1.76420.28931370.243272328602723100
1.7642-1.83480.27581600.2168267628362676100
1.8348-1.91830.24671560.2058271328692713100
1.9183-2.01940.2481270.1776273328602733100
2.0194-2.14590.20641510.1708271128622711100
2.1459-2.31160.2171500.1561270428542704100
2.3116-2.54410.1931400.163826992839269999
2.5441-2.91210.22281320.173327332865273399
2.9121-3.66830.22021530.17726932846269398
3.6683-34.33750.20311340.169727282862272897

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