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- PDB-2qwv: Crystal structure of unknown function protein VCA1059 -

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Basic information

Entry
Database: PDB / ID: 2qwv
TitleCrystal structure of unknown function protein VCA1059
ComponentsUPF0217 protein VC_A1059
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Vibrio cholerae / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


tRNA methyltransferase activity / tRNA methylation / S-adenosylmethionine-dependent methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / cytoplasm
Similarity search - Function
tRNA (pseudouridine(54)-N(1))-methyltransferase, TrmY / Putative SAM-dependent RNA methyltransferase / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / Putative pseudouridine methyltransferase
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar eltor str. N16961 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsChang, C. / Sather, A. / Moy, S. / Freeman, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of unknown function protein VCA1059.
Authors: Chang, C. / Sather, A. / Moy, S. / Freeman, L. / Joachimiak, A.
History
DepositionAug 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 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 / 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

Downloads & links

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Assembly

Deposited unit
A: UPF0217 protein VC_A1059
B: UPF0217 protein VC_A1059
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2234
Polymers47,1032
Non-polymers1202
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.514, 175.514, 42.630
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein UPF0217 protein VC_A1059


Mass: 23551.613 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar eltor str. N16961 (bacteria)
Species: Vibrio cholerae / Strain: El Tor Inaba N16961 / Gene: VC_A1059 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9KKP3
#2: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.68 Å3/Da / Density % sol: 54.15 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 35% Tacsimate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 7, 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: 2.6→50 Å / Num. all: 30250 / Num. obs: 28834 / % possible obs: 95.3 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 59.191 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 35.58
Reflection shellResolution: 2.6→2.62 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 6.19 / Num. unique all: 319 / % possible all: 78.6

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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: 2.6→41.03 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.907 / SU B: 14.271 / SU ML: 0.262 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.67 / ESU R Free: 0.328 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The Bijvoet differences were used for phasing. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26533 736 5 %RANDOM
Rwork0.20846 ---
all0.21124 13868 --
obs0.21124 13868 96.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.333 Å2
Baniso -1Baniso -2Baniso -3
1--3.78 Å2-1.89 Å20 Å2
2---3.78 Å20 Å2
3---5.67 Å2
Refinement stepCycle: LAST / Resolution: 2.6→41.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2908 0 0 48 2956
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0212957
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3531.9573996
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9125379
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.04724.18122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.7115508
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2521517
X-RAY DIFFRACTIONr_chiral_restr0.0940.2475
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022179
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2260.21301
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.22024
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.291
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2660.226
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3420.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9311.51952
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.46323048
X-RAY DIFFRACTIONr_scbond_it2.36431086
X-RAY DIFFRACTIONr_scangle_it3.5594.5948
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.665 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 52 -
Rwork0.265 849 -
obs--78.35 %
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)
111.60394.45750.45042.7013-0.04522.32480.0608-0.4007-0.85920.2597-0.1776-0.58010.6021-0.34220.1168-0.1786-0.1335-0.0346-0.15950.04540.090829.874775.978444.1561
27.10385.1535-2.84624.0188-1.31783.13260.25280.14160.95110.0007-0.21120.8357-0.0408-0.5684-0.0416-0.3004-0.10660.0230.103-0.03570.237918.624485.9841.1457
36.37553.6805-0.03593.4212-0.96070.68170.1941-0.1471-1.08580.2023-0.2735-0.74030.1596-0.27330.0794-0.1358-0.08490.0105-0.03490.00620.236335.349279.365743.0367
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 147 - 17
2X-RAY DIFFRACTION1AA51 - 6154 - 64
3X-RAY DIFFRACTION1AA65 - 7568 - 78
4X-RAY DIFFRACTION1AA103 - 118106 - 121
5X-RAY DIFFRACTION1AA132 - 181135 - 184
6X-RAY DIFFRACTION2BB16 - 5019 - 53
7X-RAY DIFFRACTION2BB81 - 10284 - 105
8X-RAY DIFFRACTION3BB119 - 131122 - 134
9X-RAY DIFFRACTION3BB182 - 203185 - 206

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