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- PDB-3dxz: Crystal structure of EcTrmB in complex with SAH -

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Basic information

Entry
Database: PDB / ID: 3dxz
TitleCrystal structure of EcTrmB in complex with SAH
ComponentstRNA (guanine-N(7)-)-methyltransferase
KeywordsTRANSFERASE / Rossmann fold methyltransferase / tRNA modification / Methyltransferase / S-adenosyl-L-methionine / tRNA processing
Function / homology
Function and homology information


tRNA (guanine-N7)-methylation / RNA (guanine-N7)-methylation / tRNA (guanine46-N7)-methyltransferase / tRNA (guanine(46)-N7)-methyltransferase activity / tRNA methyltransferase complex / tRNA methylation
Similarity search - Function
SAM-dependent methyltransferase TRMB-type domain profile. / tRNA (guanine-N-7) methyltransferase, Trmb type / Putative methyltransferase / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / tRNA (guanine-N(7)-)-methyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsZhou, H.H. / Liu, Q. / Gao, Y.X. / Teng, M.K. / Niu, L.W.
CitationJournal: Proteins / Year: 2009
Title: Monomeric tRNA (m(7)G46) methyltransferase from Escherichia coli presents a novel structure at the function-essential insertion
Authors: Zhou, H. / Liu, Q. / Yang, W. / Gao, Y. / Teng, M. / Niu, L.
History
DepositionJul 25, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tRNA (guanine-N(7)-)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5607
Polymers24,8311
Non-polymers7296
Water5,657314
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.570, 48.290, 57.480
Angle α, β, γ (deg.)90.00, 90.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein tRNA (guanine-N(7)-)-methyltransferase / tRNA(m7G46)-methyltransferase


Mass: 24831.371 Da / Num. of mol.: 1 / Fragment: UNP residues 33-239
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: trmB / Plasmid: p28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0A8I5, tRNA (guanine46-N7)-methyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.55 Å3/Da / Density % sol: 51.7 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop
Details: 15% PEG 3350 (w/v), 150 mM MgSO4, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 22, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→19.97 Å / Num. obs: 34161

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DXX

3dxx


Resolution: 1.58→19.45 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.434 / SU ML: 0.048 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19285 1693 5 %RANDOM
Rwork0.17423 ---
obs0.17517 32460 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.611 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å20.15 Å2
2--0 Å20 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 1.58→19.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1590 0 47 314 1951
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0211762
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1581.9812401
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1175228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.44924.04884
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.19715296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.2661511
X-RAY DIFFRACTIONr_chiral_restr0.0730.2252
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021365
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1980.2905
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21190
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0990.2240
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.239
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6461.51085
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.79121705
X-RAY DIFFRACTIONr_scbond_it1.3533775
X-RAY DIFFRACTIONr_scangle_it2.1424.5683
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.58→1.621 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 112 -
Rwork0.251 2358 -
obs--98.29 %
Refinement TLS params.Method: refined / Origin x: 18.3999 Å / Origin y: 3.8166 Å / Origin z: 12.3655 Å
111213212223313233
T-0.016 Å2-0.0219 Å20.0045 Å2--0.024 Å2-0.0013 Å2---0.0246 Å2
L0.4978 °2-0.1281 °20.0887 °2-0.4094 °2-0.076 °2--0.5363 °2
S-0.044 Å °0.0073 Å °0.0266 Å °0.0507 Å °0.0235 Å °0.0045 Å °0.0066 Å °-0.0284 Å °0.0205 Å °

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