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- PDB-2b25: Human putative tRNA(1-methyladenosine)methyltransferase -

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Basic information

Entry
Database: PDB / ID: 2b25
TitleHuman putative tRNA(1-methyladenosine)methyltransferase
Componentshypothetical protein
KeywordsTRANSFERASE / structural genomics / methyl transferase / sam / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


rRNA (adenine) methyltransferase activity / mRNA (adenine-N1-)-methyltransferase activity / tRNA (adenine58-N1)-methyltransferase / : / tRNA (m1A) methyltransferase complex / mitochondrial tRNA methylation / tRNA modification in the mitochondrion / : / tRNA methylation / Transferases; Transferring one-carbon groups; Methyltransferases ...rRNA (adenine) methyltransferase activity / mRNA (adenine-N1-)-methyltransferase activity / tRNA (adenine58-N1)-methyltransferase / : / tRNA (m1A) methyltransferase complex / mitochondrial tRNA methylation / tRNA modification in the mitochondrion / : / tRNA methylation / Transferases; Transferring one-carbon groups; Methyltransferases / protein homooligomerization / mitochondrial matrix / mitochondrion
Similarity search - Function
Vcp-like ATPase; Chain A, domain 2 - #20 / tRNA (1-methyladenosine) methyltransferase catalytic subunit Gcd14 / tRNA methyltransferase complex GCD14 subunit / tRNA (adenine(57)-N(1)/adenine(58)-N(1) or adenine(58)-N(1)) (EC 2.1.1.219 or EC 2.1.1.220) family profile. / Vcp-like ATPase; Chain A, domain 2 / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / tRNA (adenine(58)-N(1))-methyltransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsTempel, W. / Wu, H. / Dong, A. / Zeng, H. / Loppnau, P. / Arrowsmith, C. / Edwards, A. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. ...Tempel, W. / Wu, H. / Dong, A. / Zeng, H. / Loppnau, P. / Arrowsmith, C. / Edwards, A. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Plotnikov, A.N. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Human putative tRNA(1-methyladenosine)methyltransferase
Authors: Wu, H. / Tempel, W. / Dong, A. / Zeng, H. / Loppnau, P. / Arrowsmith, C. / Edwards, A. / Weigelt, J. / Sundstrom, M. / Bochkarev, A. / Plotnikov, A.N.
History
DepositionSep 16, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 350GENERATING THE BIOMOLECULE THE BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE IS UNKNOWN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein
B: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,3178
Polymers75,5212
Non-polymers7976
Water0
1
A: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1594
Polymers37,7601
Non-polymers3983
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1594
Polymers37,7601
Non-polymers3983
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: hypothetical protein
B: hypothetical protein
hetero molecules

A: hypothetical protein
B: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,63516
Polymers151,0414
Non-polymers1,59412
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area10110 Å2
ΔGint-49 kcal/mol
Surface area40440 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)75.533, 157.106, 113.492
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein hypothetical protein /


Mass: 37760.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET28a-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9BVS5
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 4 / Source method: obtained synthetically

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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: 2.23 Å3/Da / Density % sol: 44.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 11 % PEG3350, 0.2M lithium citrate, 0.1M BisTris, 10% PEG400, pH 6.5, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.97914 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 9, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 2.3→78.57 Å / Num. obs: 30305 / % possible obs: 99.6 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.082 / Χ2: 1.389
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Num. measured obsΧ2Diffraction-IDRmerge(I) obs
2.3-2.381005.929980.9921
2.38-2.48100629960.94610.415
2.48-2.5999.9630030.98610.341
2.59-2.73100630101.05110.238
2.73-2.9100630071.11910.164
2.9-3.12100630201.37710.115
3.12-3.441005.930441.59410.092
3.44-3.9396.84.629451.9410.077
3.93-4.951005.630801.92710.061
4.95-4099.85.232022.20610.064

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RESOLVEphasing
REFMACrefmac_5.2.0005refinement
PDB_EXTRACT1.7data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1I9G

1i9g


Resolution: 2.5→78.567 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.917 / WRfactor Rfree: 0.292 / WRfactor Rwork: 0.248 / SU B: 9.806 / SU ML: 0.22 / ESU R: 0.449 / ESU R Free: 0.294
RfactorNum. reflection% reflectionSelection details
Rfree0.2822 744 3.161 %thin shells
Rwork0.2466 ---
all0.248 ---
obs-23535 98.978 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 44.301 Å2
Baniso -1Baniso -2Baniso -3
1-3.107 Å20 Å20 Å2
2---2.692 Å20 Å2
3----0.415 Å2
Refinement stepCycle: LAST / Resolution: 2.5→78.567 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3779 0 56 0 3835
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223916
X-RAY DIFFRACTIONr_angle_refined_deg1.3661.975314
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2915482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.11423.355155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.73815624
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2641521
X-RAY DIFFRACTIONr_chiral_restr0.0830.2617
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022882
X-RAY DIFFRACTIONr_nbd_refined0.2060.21524
X-RAY DIFFRACTIONr_nbtor_refined0.30.22614
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2122
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0770.24
X-RAY DIFFRACTIONr_mcbond_it2.27722523
X-RAY DIFFRACTIONr_mcangle_it3.52233931
X-RAY DIFFRACTIONr_scbond_it2.26121608
X-RAY DIFFRACTIONr_scangle_it3.05731383
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.5650.462620.311693175899.829
2.565-2.6350.366310.29216291660100
2.635-2.7110.368620.3151594165899.879
2.711-2.7950.421620.31615311593100
2.795-2.8860.314310.28515191550100
2.886-2.9870.357620.2714341496100
2.987-3.10.365310.2441409144299.861
3.1-3.2260.283620.23913281390100
3.226-3.370.307310.26513261357100
3.37-3.5340.287310.261224127698.354
3.534-3.7240.3620.2851035123289.042
3.724-3.950.34310.241089117095.726
3.95-4.2220.247310.2081034108298.429
4.222-4.5590.199310.17610001031100
4.559-4.9920.193310.181915946100
4.992-5.5790.247310.224829860100
5.579-6.43700.24276876999.87
6.437-7.870.336310.28963466699.85
7.87-11.0740.194310.198494525100
11.074-78.56700.3730631796.53

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