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- PDB-4p7c: Crystal structure of putative methyltransferase from Pseudomonas ... -

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Basic information

Entry
Database: PDB / ID: 4p7c
TitleCrystal structure of putative methyltransferase from Pseudomonas syringae pv. tomato
ComponentstRNA (mo5U34)-methyltransferase
KeywordsTRANSFERASE / methyltransferase / PSI-BIOLOGY / structural genomics / Midwest Center for Structural Genomics / MCSG
Function / homologytRNA U34 carboxymethyltransferase / tRNA (Mo5U34)-methyltransferase-like / Protein of unknown function (DUF1698) / tRNA wobble uridine modification / Transferases; Transferring alkyl or aryl groups, other than methyl groups / transferase activity, transferring alkyl or aryl (other than methyl) groups / S-adenosyl-L-methionine-dependent methyltransferase superfamily / ACETATE ION / tRNA U34 carboxymethyltransferase
Function and homology information
Biological speciesPseudomonas syringae pv. tomato (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsChang, C. / Mack, J. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To Be Published
Title: Crystal structure of putative methyltransferase from Pseudomonas syringae pv. tomato
Authors: Chang, C. / Mack, J. / Clancy, S. / Joachimiak, A.
History
DepositionMar 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Structure summary
Revision 1.2Aug 6, 2014Group: Derived calculations
Revision 1.3Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_validate_close_contact / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tRNA (mo5U34)-methyltransferase
B: tRNA (mo5U34)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,2206
Polymers73,8332
Non-polymers3864
Water8,989499
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint5 kcal/mol
Surface area27140 Å2
Unit cell
Length a, b, c (Å)64.076, 88.732, 128.094
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

#1: Protein tRNA (mo5U34)-methyltransferase


Mass: 36916.645 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. tomato (bacteria)
Strain: DC3000 / Gene: cmoB, PSPTO_4213 / Plasmid: pMCSG57 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic
References: UniProt: Q87XG5, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


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


Mass: 18.015 Da / Num. of mol.: 499 / Source method: isolated from a natural source / Formula: H2O

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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: 2.5 Å3/Da / Density % sol: 50.76 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.2M Ammonium Acetate, 0.1M Bis-Tris, 25% PEG3350

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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 315r / Detector: CCD / Date: Mar 25, 2012
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 62685 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Rmerge(I) obs: 0.188 / Net I/av σ(I): 16 / Net I/σ(I): 5.4
Reflection shellResolution: 1.85→1.87 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.956 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.85→35.08 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.23 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.258 / ESU R Free: 0.116
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1967 3162 5.1 %RANDOM
Rwork0.1517 59192 --
obs0.154 62354 99.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 67.67 Å2 / Biso mean: 12.557 Å2 / Biso min: 3.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å20 Å2
2---0.47 Å20 Å2
3---0.02 Å2
Refinement stepCycle: final / Resolution: 1.85→35.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5110 0 26 499 5635
Biso mean--32.09 25.14 -
Num. residues----641
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.025442
X-RAY DIFFRACTIONr_angle_refined_deg1.3581.9587435
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6485675
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.13623.49255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.14515890
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.7961544
X-RAY DIFFRACTIONr_chiral_restr0.090.2797
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214256
X-RAY DIFFRACTIONr_rigid_bond_restr2.06435442
X-RAY DIFFRACTIONr_sphericity_free26.6785144
X-RAY DIFFRACTIONr_sphericity_bonded7.77355641
LS refinement shellResolution: 1.852→1.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 206 -
Rwork0.186 3748 -
all-3954 -
obs--92.28 %
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)
11.68061.46780.16786.9194-0.31143.6485-0.0446-0.0137-0.1981-0.37770.0141-0.3190.16780.0240.03050.05030.00130.02970.0036-0.00310.04544.384550.8255-4.5334
21.40350.171-0.05760.6474-0.17210.42070.0042-0.025-0.1886-0.0820.0203-0.03540.0632-0.0678-0.02450.0399-0.0015-0.01290.0189-0.00210.046423.422941.0939-4.3374
30.18890.03890.05360.18540.12550.3760.0028-0.009-0.0152-0.0002-0.00280.0007-0.0112-0.012100.0311-0.00030.0010.03040.00820.03325.096757.73047.72
43.71820.7931-2.25070.6864-0.90561.71390.1223-0.1240.2450.08130.00840.0357-0.11380.0389-0.13060.0387-0.02250.00940.0567-0.02610.025721.753964.853414.4167
53.1884-0.0937-1.03314.68460.57254.640.15340.2246-0.35620.0145-0.09530.18710.2181-0.4555-0.05820.0392-0.048-0.02770.1363-0.01540.05617.97283.212521.0366
61.01730.03120.34291.709-0.53690.9862-0.0205-0.07120.1136-0.04590.03280.2834-0.0721-0.1911-0.01230.01230.0102-0.01540.083-0.00480.06162.28225.013216.7511
70.40290.06460.31860.26550.00650.5308-0.01020.01110.0061-0.00190.01180.02730.0155-0.0119-0.00150.04040.0008-0.00360.020.00110.020321.628322.506923.0654
80.1002-0.0198-0.05596.76721.71951.73590.0013-0.0345-0.0247-0.19120.0711-0.1076-0.08890.1012-0.07230.01650.002-0.01950.0308-0.0050.073831.082425.623325.9506
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 22
2X-RAY DIFFRACTION2A23 - 90
3X-RAY DIFFRACTION3A91 - 301
4X-RAY DIFFRACTION4A302 - 319
5X-RAY DIFFRACTION5B1 - 22
6X-RAY DIFFRACTION6B23 - 90
7X-RAY DIFFRACTION7B91 - 301
8X-RAY DIFFRACTION8B302 - 319

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