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- PDB-1v2x: TrmH -

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Basic information

Entry
Database: PDB / ID: 1v2x
TitleTrmH
ComponentstRNA (Gm18) methyltransferase
KeywordsTRANSFERASE / deep trefoil knot / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


tRNA (guanosine18-2'-O)-methyltransferase / tRNA guanine ribose methylation / : / tRNA binding
Similarity search - Function
RNA methyltransferase, SpoU/TrmH type, C-terminal / tRNA (guanosine(18)-2'-O)-methyltransferase / SpoU, rRNA methylase, C-terminal / tRNA/rRNA methyltransferase, SpoU type / SpoU rRNA Methylase family / 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
PHOSPHATE ION / S-ADENOSYLMETHIONINE / tRNA (guanosine(18)-2'-O)-methyltransferase / tRNA (guanosine(18)-2'-O)-methyltransferase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsNureki, O. / Watanabe, K. / Fukai, S. / Ishii, R. / Endo, Y. / Hori, H. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: STRUCTURE / Year: 2004
Title: Deep Knot Structure for Construction of Active Site and Cofactor Binding Site of tRNA Modification Enzyme
Authors: Nureki, O. / Watanabe, K. / Fukai, S. / Ishii, R. / Endo, Y. / Hori, H. / Yokoyama, S.
History
DepositionOct 17, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 4, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jun 26, 2013Group: Derived calculations
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: tRNA (Gm18) methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7094
Polymers22,1201
Non-polymers5883
Water3,423190
1
A: tRNA (Gm18) methyltransferase
hetero molecules

A: tRNA (Gm18) methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4188
Polymers44,2412
Non-polymers1,1776
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4290 Å2
ΔGint-45 kcal/mol
Surface area16570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.601, 44.023, 56.756
Angle α, β, γ (deg.)90.00, 120.78, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein tRNA (Gm18) methyltransferase


Mass: 22120.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9FAC4, UniProt: Q5SM16*PLUS, tRNA (guanosine18-2'-O)-methyltransferase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 1.69 Å3/Da / Density % sol: 26.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: lithium sulfate, Tris-HCl, PEG 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 26, 2002 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.5→40 Å / Num. all: 65676 / Num. obs: 60955 / % possible obs: 91.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Biso Wilson estimate: 18 Å2 / Rsym value: 0.047 / Net I/σ(I): 9.5
Reflection shellHighest resolution: 1.5 Å / Mean I/σ(I) obs: 1.6 / Num. unique all: 24289 / Rsym value: 0.252 / % possible all: 81.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.5→34.37 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1127109.35 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.277 2399 9.9 %RANDOM
Rwork0.225 ---
all0.229 ---
obs0.225 24289 91.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 85.9434 Å2 / ksol: 0.399441 e/Å3
Displacement parametersBiso mean: 32.3 Å2
Baniso -1Baniso -2Baniso -3
1--6.86 Å20 Å2-2.38 Å2
2--13.51 Å20 Å2
3----6.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.57 Å
Refinement stepCycle: LAST / Resolution: 1.5→34.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1530 0 37 190 1757
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d1.14
X-RAY DIFFRACTIONc_mcbond_it2.721.5
X-RAY DIFFRACTIONc_mcangle_it3.542
X-RAY DIFFRACTIONc_scbond_it4.72
X-RAY DIFFRACTIONc_scangle_it5.972.5
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.533 362 10.2 %
Rwork0.538 3172 -
obs--80.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4SAM2.PARAMSAM2.TOP

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