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- PDB-2oyz: Crystal structure of unknown function protein VPA0057 from Vibrio... -

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Basic information

Entry
Database: PDB / ID: 2oyz
TitleCrystal structure of unknown function protein VPA0057 from Vibrio parahaemolyticus (targeted domain 2-94)
ComponentsUPF0345 protein VPA0057
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Vibrio parahaemolyticus / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


pyrimidine-nucleoside phosphorylase / thymidine phosphorylase activity / uridine phosphorylase activity / guanosine phosphorylase activity / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / cytosol
Similarity search - Function
Pyrimidine/purine nucleoside phosphorylase / Pyrimidine/purine nucleoside phosphorylase / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Pyrimidine/purine nucleoside phosphorylase
Similarity search - Component
Biological speciesVibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.71 Å
AuthorsChang, C. / Volkart, L. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of unknown function protein VPA0057 from Vibrio parahaemolyticus
Authors: Chang, C. / Volkart, L. / Abdullah, J. / Joachimiak, A.
History
DepositionFeb 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2007Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UPF0345 protein VPA0057


Theoretical massNumber of molelcules
Total (without water)10,2541
Polymers10,2541
Non-polymers00
Water1,874104
1
A: UPF0345 protein VPA0057

A: UPF0345 protein VPA0057


Theoretical massNumber of molelcules
Total (without water)20,5082
Polymers20,5082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Unit cell
Length a, b, c (Å)37.302, 37.302, 135.555
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-95-

HOH

Detailsprobable dimer with operator (x,y,z) and (-x,y,-z)

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Components

#1: Protein UPF0345 protein VPA0057


Mass: 10254.017 Da / Num. of mol.: 1 / Fragment: Residues 2-94
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Strain: RIMD 2210633 / Gene: VPA0057 / Plasmid: pMCSG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) derivatives / References: UniProt: Q87K41
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.49 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1M CaCl2, 0.1M Sodium acetate pH 4.6, 15% PEG 400, 10% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 2, 2006
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.71→50 Å / Num. all: 11162 / Num. obs: 11064 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 13.4 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 72
Reflection shellResolution: 1.71→1.77 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 4.52 / Num. unique all: 1003 / % possible all: 93.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.71→37.29 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.937 / SU B: 5.182 / SU ML: 0.085 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23657 528 4.8 %RANDOM
Rwork0.20298 ---
all0.20461 10480 --
obs0.20461 10480 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.536 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å20 Å2
2--0.41 Å20 Å2
3----0.82 Å2
Refinement stepCycle: LAST / Resolution: 1.71→37.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms711 0 0 104 815
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022839
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4811.9321150
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1485118
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.6925.36641
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.11415136
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.031153
X-RAY DIFFRACTIONr_chiral_restr0.0990.2122
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02676
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2250.2298
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.2547
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.281
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.259
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2010.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9041.5540
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.2932856
X-RAY DIFFRACTIONr_scbond_it2.3943339
X-RAY DIFFRACTIONr_scangle_it3.074.5289
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.71→1.756 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 31 -
Rwork0.235 727 -
obs--95.95 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.063-0.59021.25390.4311-0.5153.8232-0.0695-0.2194-0.32090.0441-0.02970.02010.25080.01880.0992-0.0602-0.009-0.0192-0.06060.0282-0.02242.07694.38455.3058
22.1058-0.02630.17841.9971-0.94333.4994-0.0157-0.0763-0.00180.31170.09870.045-0.2226-0.2773-0.083-0.05770.0475-0.00320.02140.0096-0.0668-9.098713.214315.5483
33.122-0.0577-0.88912.5466-1.03954.9606-0.0482-0.01470.06510.23590.0033-0.1954-0.27940.14690.0449-0.0615-0.0006-0.0389-0.03230.0189-0.0673-0.9614.70259.792
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 321 - 32
2X-RAY DIFFRACTION2AA33 - 4033 - 40
3X-RAY DIFFRACTION2AA50 - 6750 - 67
4X-RAY DIFFRACTION2AA76 - 8476 - 84
5X-RAY DIFFRACTION3AA41 - 4941 - 49
6X-RAY DIFFRACTION3AA68 - 7568 - 75
7X-RAY DIFFRACTION3AA85 - 9485 - 94

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