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- PDB-2qhq: Crystal structure of unknown function protein VPA0580 -

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Basic information

Entry
Database: PDB / ID: 2qhq
TitleCrystal structure of unknown function protein VPA0580
ComponentsUnknown function protein VPA0580
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Vibrio parahaemolyticus / unknown function protein / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologypseudo Tubby roll / vpa0580 domain like / HopJ type III effector protein / Type III effector HopJ superfamily / HopJ type III effector protein / Alpha-Beta Barrel / Alpha Beta / ACETATE ION / Type III effector
Function and homology information
Biological speciesVibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.76 Å
AuthorsChang, C. / Kim, Y. / Volkart, L. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of unknown function protein VPA0580.
Authors: Chang, C. / Kim, Y. / Volkart, L. / Abdullah, J. / Joachimiak, A.
History
DepositionJul 2, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 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 1.3Mar 26, 2025Group: 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Unknown function protein VPA0580
B: Unknown function protein VPA0580
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7013
Polymers28,6422
Non-polymers591
Water4,972276
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.796, 80.851, 87.774
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 Unknown function protein VPA0580


Mass: 14321.166 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Strain: RIMD 2210633 / Gene: VPA0580 / Plasmid: pMCSG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) derivative / References: UniProt: Q87IM6
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.15 Å3/Da / Density % sol: 42.92 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.8 M Sodium acetate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97918 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Apr 16, 2007
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. all: 25661 / Num. obs: 25191 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 16.83 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 44.87
Reflection shellResolution: 1.76→1.82 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 14.55 / % possible all: 97.4

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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: 1.76→30.03 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.041 / SU ML: 0.069 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20926 1285 5.1 %RANDOM
Rwork0.17009 ---
obs0.17215 23845 99.38 %-
all-23845 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.78 Å20 Å20 Å2
2--0.65 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.76→30.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1927 0 4 276 2207
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222024
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3091.9662747
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9455256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.82426.106113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.24415295
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.017156
X-RAY DIFFRACTIONr_chiral_restr0.0910.2294
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021624
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1890.2959
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21425
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2226
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.220.278
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1310.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8771.51262
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.20721966
X-RAY DIFFRACTIONr_scbond_it2.3393843
X-RAY DIFFRACTIONr_scangle_it3.5044.5772
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.76→1.806 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 97 -
Rwork0.179 1679 -
obs--97.85 %
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)
18.47177.45953.98056.56823.50491.8703-0.18910.98430.1372-0.27520.3705-0.0052-0.20880.2825-0.18140.0305-0.01040.00960.05760.03460.061433.050676.82459.2534
20.5243-0.05440.28620.60180.14651.31410.03410.0311-0.0240.0288-0.0053-0.03470.04030.0083-0.0287-0.0246-0.00310.0083-0.0195-0.0057-0.023334.589259.676610.1603
33.3781-2.44890.13262.53280.11230.66430.0076-0.1062-0.0127-0.0329-0.01590.15260.0519-0.06240.0083-0.0242-0.0310.0144-0.0277-0.0072-0.028127.298545.049531.3068
40.9555-0.2789-0.30780.53310.18090.5698-0.01210.02810.04180.0312-0.0033-0.0125-0.0079-0.04570.0154-0.01710.0002-0.0059-0.01750.0033-0.023826.969261.749933.95
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 246 - 27
2X-RAY DIFFRACTION2AA25 - 12228 - 125
3X-RAY DIFFRACTION3BB1 - 244 - 27
4X-RAY DIFFRACTION4BB25 - 12228 - 125

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