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- PDB-2w3y: Structure of the Evf virulence factor -

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Basic information

Entry
Database: PDB / ID: 2w3y
TitleStructure of the Evf virulence factor
ComponentsVIRULENCE FACTOR
KeywordsLIPID BINDING PROTEIN / DROSOPHILA PATHOGEN / ERWINIA CAROTOVORA / S-PALMITOYLATED PROTEIN / LIPID-BINDING PROTEIN
Function / homologyVirulence factor Evf / Virulence factor Evf / PALMITIC ACID / Virulence factor
Function and homology information
Biological speciesPECTOBACTERIUM CAROTOVORUM SUBSP. CAROTOVORUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsQuevillon-Cheruel, S. / Leulliot, N. / Acosta Muniz C, C. / Vincent, M. / Gallay, J. / Argentini, M. / Cornu, D. / Boccard, F. / Lemaitre, B. / van Tilbeurgh, H.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Evf, a Virulence Factor Produced by the Drosophila Pathogen Erwinia Carotovora is a S-Palmitoylated Protein with a New Fold that Binds to Lipid Vesicles.
Authors: Quevillon-Cheruel, S. / Leulliot, N. / Acosta Muniz, C. / Vincent, M. / Gallay, J. / Argentini, M. / Cornu, D. / Boccard, F. / Lemaitre, B. / Van Tilbeurgh, H.
History
DepositionNov 17, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 30, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VIRULENCE FACTOR
B: VIRULENCE FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0094
Polymers64,4962
Non-polymers5132
Water6,521362
1
A: VIRULENCE FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5042
Polymers32,2481
Non-polymers2561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: VIRULENCE FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5042
Polymers32,2481
Non-polymers2561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.560, 86.715, 91.457
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein VIRULENCE FACTOR / EVF


Mass: 32247.908 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PECTOBACTERIUM CAROTOVORUM SUBSP. CAROTOVORUM (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21-GOLD(DE3) / References: UniProt: Q8GCR2
#2: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.59 % / Description: NONE
Crystal growDetails: 25% PEG4000, 50MM BICINE PH 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9798
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2→80 Å / Num. obs: 38113 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 27.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 25.6

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Processing

SoftwareName: REFMAC / Version: 5.2.0005 / Classification: refinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2→62.87 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.721 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1900 5 %RANDOM
Rwork0.2 ---
obs0.203 36142 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.19 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2---0.11 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 2→62.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4247 0 32 362 4641
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224380
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1791.9325903
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8455524
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.49825.451233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.86115721
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.578159
X-RAY DIFFRACTIONr_chiral_restr0.0840.2618
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023387
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1880.21785
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.22986
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2304
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1510.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1130.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7061.52691
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.19724205
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.75431926
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7134.51698
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.394 142
Rwork0.273 2611

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