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- PDB-2v1l: Structure of the conserved hypothetical protein VC1805 from patho... -

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Basic information

Entry
Database: PDB / ID: 2v1l
TitleStructure of the conserved hypothetical protein VC1805 from pathogenicity island VPI-2 of Vibrio cholerae O1 biovar eltor str. N16961 shares structural homology with the human P32 protein
ComponentsHYPOTHETICAL PROTEIN
KeywordsUNKNOWN FUNCTION / PATHOGENICITY ISLAND / HYPOTHETICAL PROTEIN
Function / homologyProtein of unknown function DUF2787 / Protein of unknown function DUF2787 / Protein of unknown function (DUF2787) / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / DUF2787 domain-containing protein
Function and homology information
Biological speciesVIBRIO CHOLERAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.13 Å
AuthorsSheikh, M.A. / Potter, J.A. / Johnson, K.A. / Boyd, E.F. / Taylor, G.L.
CitationJournal: Proteins / Year: 2008
Title: Crystal Structure of Vc1805, a Conserved Hypothetical Protein from a Vibrio Cholerae Pathogenicity Island, Reveals Homology to Human P32.
Authors: Sheikh, M.A. / Potter, J.A. / Johnson, K.A. / Sim, R.B. / Boyd, E.F. / Taylor, G.L.
History
DepositionMay 25, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HYPOTHETICAL PROTEIN


Theoretical massNumber of molelcules
Total (without water)16,8471
Polymers16,8471
Non-polymers00
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)78.312, 78.312, 42.288
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 HYPOTHETICAL PROTEIN / HYPOTHETICAL PROTEIN VC1805


Mass: 16846.613 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) VIBRIO CHOLERAE (bacteria) / Strain: O1 / Variant: BIOVAR ELTOR STR. N16961 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9KR41
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 44 % / Description: NONE
Crystal growpH: 7.5 / Details: pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.13→39.16 Å / Num. obs: 8131 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 8.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 23
Reflection shellResolution: 2.13→2.25 Å / Redundancy: 9 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 6.4 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
SOLVE/RESOLVEphasing
RefinementMethod to determine structure: MIRAS
Starting model: NONE

Resolution: 2.13→39.16 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.871 / SU B: 6.663 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.274 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.316 409 4.8 %RANDOM
Rwork0.235 ---
obs0.239 8131 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.21 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0.13 Å20 Å2
2---0.25 Å20 Å2
3---0.38 Å2
Refinement stepCycle: LAST / Resolution: 2.13→39.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1054 0 0 35 1089
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221086
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3861.9211476
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3035126
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.61224.09861
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.76515158
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.619155
X-RAY DIFFRACTIONr_chiral_restr0.0990.2153
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02865
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2290.2420
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.2704
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.243
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3540.235
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2140.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1351.5666
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.98721030
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9983496
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9244.5446
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: 2.13→2.19 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.347 32
Rwork0.247 586

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