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- PDB-5dyr: Structure of virulence-associated protein D (VapD) from Xylella f... -

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Basic information

Entry
Database: PDB / ID: 5dyr
TitleStructure of virulence-associated protein D (VapD) from Xylella fastidiosa
ComponentsVirulence-associated protein D
KeywordsDNA BINDING PROTEIN / VapD / Virulence-associated protein D / Xylella fastidiosa / cell invasion
Function / homologyVirulence-associated protein D / CRISPR associated protein Cas2 / CRISPR associated protein Cas2 / nuclease activity / Virulence-associated protein D
Function and homology information
Biological speciesXylella fastidiosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKochneva, M.V. / dos Santos, M.L. / dos Santos, C.A. / de Souza, A.P. / Polikarpov, I. / Aparicio, R. / Golubev, A.M.
CitationJournal: To Be Published
Title: Structure of virulence-associated protein D (VapD) from Xylella fastidiosa
Authors: Kochneva, M.V. / dos Santos, M.L. / dos Santos, C.A. / de Souza, A.P. / Polikarpov, I. / Aparicio, R. / Golubev, A.M.
History
DepositionSep 25, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1May 8, 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: Virulence-associated protein D


Theoretical massNumber of molelcules
Total (without water)17,6591
Polymers17,6591
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.930, 107.930, 53.281
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Virulence-associated protein D


Mass: 17658.842 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xylella fastidiosa (strain 9a5c) (bacteria)
Strain: 9a5c / Gene: XF_a0052 / Plasmid: pET32Xa/LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9PHF6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 20% MPD, 0.1M NaAc pH 4.5, 170mM glycine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4586 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 11, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4586 Å / Relative weight: 1
ReflectionResolution: 2.2→35.1 Å / Num. obs: 15925 / % possible obs: 85.8 % / Redundancy: 11.4 % / Rsym value: 0.218 / Net I/σ(I): 6.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
PHASERphasing
XDSdata scaling
CNSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→18.69 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.897 / SU B: 7.291 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25306 325 5 %RANDOM
Rwork0.19914 ---
obs0.20183 6117 87.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.259 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20 Å2
2--0.15 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 3→18.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1153 0 0 8 1161
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191191
X-RAY DIFFRACTIONr_bond_other_d0.0030.021120
X-RAY DIFFRACTIONr_angle_refined_deg1.7221.9211608
X-RAY DIFFRACTIONr_angle_other_deg1.06932547
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6775142
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.62123.56273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.48715210
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7641513
X-RAY DIFFRACTIONr_chiral_restr0.090.2170
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021396
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02327
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.1076.055559
X-RAY DIFFRACTIONr_mcbond_other5.0976.051558
X-RAY DIFFRACTIONr_mcangle_it7.7789.061698
X-RAY DIFFRACTIONr_mcangle_other7.7789.064699
X-RAY DIFFRACTIONr_scbond_it4.7136.02631
X-RAY DIFFRACTIONr_scbond_other4.7136.019631
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.9089.026908
X-RAY DIFFRACTIONr_long_range_B_refined11.03747.6481447
X-RAY DIFFRACTIONr_long_range_B_other11.03447.6671448
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.001→3.079 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.192 9 -
Rwork0.179 282 -
obs--54.8 %

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