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- PDB-3ief: Crystal structure of tRNA guanine-n1-methyltransferase from Barto... -

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Basic information

Entry
Database: PDB / ID: 3ief
TitleCrystal structure of tRNA guanine-n1-methyltransferase from Bartonella henselae using MPCS.
ComponentstRNA (guanine-N(1)-)-methyltransferase
KeywordsTRANSFERASE / RNA BINDING PROTEIN / NIAID / SSGCID / Seattle Structural Genomics Center for Infectious Diseases / Microcapillary Protein Crystallization System / MPCS / PSI-2 / Protein Structure Initiative / Accelerated Technologies Center for Gene to 3D Structure / ATCG3D / Cytoplasm / Methyltransferase / S-adenosyl-L-methionine / tRNA processing / protein knot
Function / homology
Function and homology information


tRNA (guanine37-N1)-methyltransferase / tRNA (guanine(37)-N1)-methyltransferase activity / tRNA modification / methylation / cytoplasm
Similarity search - Function
tRNA(m1g37)methyltransferase, domain 2 / Trp Operon Repressor; Chain A / tRNA (guanine-N1-)-methyltransferase, bacteria / tRNA (guanine-N(1)-)-methyltransferase, C-terminal domain superfamily / tRNA methyltransferase TRMD/TRM10-type domain / tRNA (Guanine-1)-methyltransferase / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases ...tRNA(m1g37)methyltransferase, domain 2 / Trp Operon Repressor; Chain A / tRNA (guanine-N1-)-methyltransferase, bacteria / tRNA (guanine-N(1)-)-methyltransferase, C-terminal domain superfamily / tRNA methyltransferase TRMD/TRM10-type domain / tRNA (Guanine-1)-methyltransferase / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
tRNA (guanine-N(1)-)-methyltransferase
Similarity search - Component
Biological speciesBartonella henselae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsEdwards, T.E. / Stahl, G. / Gerdts, C.J. / Staker, B.L. / Accelerated Technologies Center for Gene to 3D Structure (ATCG3D) / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of tRNA guanine-n1-methyltransferase from Bartonella henselae using MPCS.
Authors: Edwards, T.E. / Stahl, G. / Gerdts, C.J. / Staker, B.L. / Accelerated Technologies Center for Gene to 3D Structure (ATCG3D) / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionJul 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tRNA (guanine-N(1)-)-methyltransferase
B: tRNA (guanine-N(1)-)-methyltransferase


Theoretical massNumber of molelcules
Total (without water)51,1622
Polymers51,1622
Non-polymers00
Water1,67593
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6650 Å2
ΔGint-21 kcal/mol
Surface area19170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.017, 84.467, 97.192
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein tRNA (guanine-N(1)-)-methyltransferase / M1G-methyltransferase / tRNA [GM37] methyltransferase


Mass: 25581.215 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Expressed as a fusion protein with H-terminal hexahis tag and Smt3 protein. Cleaved with ULP-1 protease, then purified as target protein with only one Ser from expression tag.
Source: (gene. exp.) Bartonella henselae (bacteria) / Strain: Houston-1 / Gene: trmD, BH15820 / Plasmid: pBADSmt / Production host: Escherichia coli (E. coli) / References: UniProt: Q6G1R9, EC: 2.1.1.31
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.25 Å3/Da / Density % sol: 45.26 %
Crystal growTemperature: 293 K / Method: mpcs / pH: 7
Details: Initial crystal hit JCSG+ condition G7 15% PEG 3350, 0.1M succinic acid pH 7.0 optimized with microcapillary gradient, MPCS, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97946 Å
DetectorDate: Jun 19, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 16569 / % possible obs: 99.9 % / Redundancy: 8.9 % / Rmerge(I) obs: 0.116 / Χ2: 0.997 / Net I/σ(I): 18.2
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 3.8 / Num. unique all: 1614 / Χ2: 0.987 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 50.97 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å38.73 Å
Translation3 Å38.73 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1p9p

1p9p


Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.936 / WRfactor Rfree: 0.199 / WRfactor Rwork: 0.173 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.847 / SU B: 8.475 / SU ML: 0.191 / SU R Cruickshank DPI: 0.619 / SU Rfree: 0.266 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.619 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.225 825 5 %RANDOM
Rwork0.195 ---
obs0.196 16525 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 67.43 Å2 / Biso mean: 30.164 Å2 / Biso min: 8.67 Å2
Baniso -1Baniso -2Baniso -3
1--0.99 Å20 Å20 Å2
2---1.98 Å20 Å2
3---2.97 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3287 0 0 93 3380
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223349
X-RAY DIFFRACTIONr_angle_refined_deg1.3811.9784544
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0395434
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.11222.897145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.45515526
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3051534
X-RAY DIFFRACTIONr_chiral_restr0.0840.2514
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212569
X-RAY DIFFRACTIONr_mcbond_it0.781.52173
X-RAY DIFFRACTIONr_mcangle_it1.47123445
X-RAY DIFFRACTIONr_scbond_it1.99931176
X-RAY DIFFRACTIONr_scangle_it3.2964.51099
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 49 -
Rwork0.239 1136 -
all-1185 -
obs--99.33 %

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