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- PDB-2w56: Structure of the hypothetical protein VC0508 from Vibrio cholerae... -

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Basic information

Entry
Database: PDB / ID: 2w56
TitleStructure of the hypothetical protein VC0508 from Vibrio cholerae VSP- II pathogenicity island
Components(VC0508) x 2
KeywordsUNKNOWN FUNCTION
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSheikh, M.A. / Taylor, G.L.
CitationJournal: To be Published
Title: Structure of the Hypothetical Protein Vc0508 from Vibrio Cholerae Vsp-II Pathogenicity Island
Authors: Sheikh, M.A. / Taylor, G.L.
History
DepositionDec 5, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
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: VC0508
B: VC0508


Theoretical massNumber of molelcules
Total (without water)34,0442
Polymers34,0442
Non-polymers00
Water3,495194
1
A: VC0508


Theoretical massNumber of molelcules
Total (without water)17,0221
Polymers17,0221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: VC0508


Theoretical massNumber of molelcules
Total (without water)17,0221
Polymers17,0221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)41.102, 70.596, 51.382
Angle α, β, γ (deg.)90.00, 110.64, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein VC0508


Mass: 17022.184 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) VIBRIO CHOLERAE (bacteria) / Strain: N16961 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9KUL0
#2: Protein VC0508


Mass: 17022.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) VIBRIO CHOLERAE (bacteria) / Strain: N16961 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9KUL0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.05 Å3/Da / Density % sol: 40 % / Description: NONE
Crystal growpH: 5.5 / Details: PH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU SATURN 944 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 21026 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 62
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.03 / Mean I/σ(I) obs: 5.6 / % possible all: 96

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V1L

2v1l


Resolution: 1.9→48.06 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.916 / SU B: 9.055 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1065 5.1 %RANDOM
Rwork0.224 ---
obs0.227 19870 96.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å20.57 Å2
2--0.64 Å20 Å2
3----0.79 Å2
Refinement stepCycle: LAST / Resolution: 1.9→48.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2247 0 0 194 2441
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222309
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3391.9373124
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5425270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.2123.445119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.12515372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6281513
X-RAY DIFFRACTIONr_chiral_restr0.0960.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021789
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1970.2972
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21575
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2188
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.263
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2240.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9011.51403
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.49122174
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.12231074
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2994.5950
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: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.301 65
Rwork0.266 1419
Refinement TLS params.Method: refined / Origin x: 27.178 Å / Origin y: 6.623 Å / Origin z: -3.871 Å
111213212223313233
T-0.0102 Å20.0217 Å2-0.0212 Å2--0.0195 Å20.0097 Å2--0.0088 Å2
L0.7692 °20.2701 °2-0.74 °2-0.1013 °2-0.3296 °2--1.4644 °2
S0.0179 Å °-0.0298 Å °-0.0316 Å °-0.0158 Å °-0.0422 Å °-0.002 Å °0.1228 Å °0.0826 Å °0.0243 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 83
2X-RAY DIFFRACTION1A86 - 147
3X-RAY DIFFRACTION1B5 - 28
4X-RAY DIFFRACTION1B40 - 146

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