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- PDB-1r6f: The structure of Yersinia pestis V-antigen, an essential virulenc... -

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Basic information

Entry
Database: PDB / ID: 1r6f
TitleThe structure of Yersinia pestis V-antigen, an essential virulence factor and mediator of immunity against plague
ComponentsVirulence-associated V antigen
KeywordsPROTEIN BINDING / coiled-coil
Function / homologyLow calcium response V antigen / Virulence-associated V antigen superfamily / V antigen (LcrV) protein / : / extracellular region / Virulence-associated V antigen / Virulence-associated V antigen
Function and homology information
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.17 Å
AuthorsDerewenda, U. / Mateja, A. / Devedjiev, Y. / Routzahn, K.M. / Evdokimov, A.G. / Derewenda, Z.S. / Waugh, D.S.
CitationJournal: Structure / Year: 2004
Title: The structure of Yersinia pestis V-antigen, an essential virulence factor and mediator of immunity against plague
Authors: Derewenda, U. / Mateja, A. / Devedjiev, Y. / Routzahn, K.M. / Evdokimov, A.G. / Derewenda, Z.S. / Waugh, D.S.
History
DepositionOct 15, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Virulence-associated V antigen


Theoretical massNumber of molelcules
Total (without water)35,1591
Polymers35,1591
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.881, 45.086, 46.915
Angle α, β, γ (deg.)76.20, 78.42, 77.17
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 35158.555 Da / Num. of mol.: 1 / Fragment: Lcrv fragment 24-323 / Mutation: K40A D41A K42A C273S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Plasmid: MBP-LCRV(DELTA1-23-C273S)-HIS6 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: P21206, UniProt: P0C7U7*PLUS

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.07 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: PEG 5000 MME, sodium acetate, Tris, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
126 %(w/v)PEG5000 MME1reservoir
2200 mMsodium acetate1reservoir
3100 mMTris-HCl1reservoirpH8.7
430 mg/mlprotein1drop

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X9A10.9795, 0.9790, 0.9719
SYNCHROTRONNSLS X9B20.9715
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDJan 15, 2002
ADSC QUANTUM 42CCDJan 15, 2002
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.9791
30.97191
40.97151
ReflectionResolution: 2.17→18.5 Å / Num. all: 14116 / Num. obs: 14116 / % possible obs: 95.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 12.5
Reflection shellResolution: 2.17→2.25 Å / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2 / % possible all: 86.2
Reflection
*PLUS
Num. measured all: 31607
Reflection shell
*PLUS
% possible obs: 86.2 % / Rmerge(I) obs: 0.37

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.17→18.5 Å / Cor.coef. Fo:Fc: 0.941 / Isotropic thermal model: Isotropic / σ(F): 0 / ESU R: 0.398
RfactorNum. reflection% reflectionSelection details
Rfree0.284 1383 -Random
Rwork0.217 ---
all0.224 14116 --
obs0.224 14116 96.22 %-
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: 27.251 Å2
Baniso -1Baniso -2Baniso -3
1--2.29 Å22.2 Å2-1.8 Å2
2---0.4 Å2-2.91 Å2
3---3.82 Å2
Refinement stepCycle: LAST / Resolution: 2.17→18.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2139 0 0 0 2139
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0212163
X-RAY DIFFRACTIONr_angle_refined_deg1.8771.9652909
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2375268
X-RAY DIFFRACTIONr_chiral_restr0.1310.2339
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021576
X-RAY DIFFRACTIONr_nbd_refined0.3070.21355
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2630.2260
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2470.275
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.220.233
X-RAY DIFFRACTIONr_mcbond_it0.6291.51345
X-RAY DIFFRACTIONr_mcangle_it1.08822165
X-RAY DIFFRACTIONr_scbond_it2.1243818
X-RAY DIFFRACTIONr_scangle_it3.0684.5744
LS refinement shellResolution: 2.17→2.207 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rwork0.343 792
Rfree-0
Refinement
*PLUS
Lowest resolution: 30 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.008
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.877

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