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- PDB-1i9g: CRYSTAL STRUCTURE OF AN ADOMET DEPENDENT METHYLTRANSFERASE -

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Basic information

Entry
Database: PDB / ID: 1i9g
TitleCRYSTAL STRUCTURE OF AN ADOMET DEPENDENT METHYLTRANSFERASE
ComponentsHYPOTHETICAL PROTEIN RV2118CHypothesis
KeywordsTRANSFERASE / mycobacterium / MTase / AdoMet / crystal / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


tRNA (adenine58-N1)-methyltransferase / : / tRNA (m1A) methyltransferase complex / tRNA methylation / S-adenosylmethionine-dependent methyltransferase activity / plasma membrane
Similarity search - Function
TrmI-like N-terminal / 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 ...TrmI-like N-terminal / 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 TrmI / tRNA (adenine(58)-N(1))-methyltransferase TrmI
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.98 Å
AuthorsGupta, A. / Kumar, P.H. / Dineshkumar, T.K. / Varshney, U. / Subramanya, H.S. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Crystal structure of Rv2118c: an AdoMet-dependent methyltransferase from Mycobacterium tuberculosis H37Rv.
Authors: Gupta, A. / Kumar, P.H. / Dineshkumar, T.K. / Varshney, U. / Subramanya, H.S.
History
DepositionMar 20, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 26, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Nov 21, 2018Group: Data collection / Category: reflns / Item: _reflns.pdbx_Rsym_value
Revision 1.5Mar 13, 2024Group: 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: HYPOTHETICAL PROTEIN RV2118C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5592
Polymers30,1611
Non-polymers3981
Water2,972165
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: HYPOTHETICAL PROTEIN RV2118C
hetero molecules

A: HYPOTHETICAL PROTEIN RV2118C
hetero molecules

A: HYPOTHETICAL PROTEIN RV2118C
hetero molecules

A: HYPOTHETICAL PROTEIN RV2118C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,2368
Polymers120,6424
Non-polymers1,5944
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area13160 Å2
ΔGint-69 kcal/mol
Surface area41130 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)66.420, 86.790, 138.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein HYPOTHETICAL PROTEIN RV2118C / Hypothesis


Mass: 30160.506 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: RV2118C / Plasmid: PQE60 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: O33253, UniProt: P9WFZ1*PLUS
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


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


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.3 Å3/Da / Density % sol: 62.7 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15-6 mg/mlprotein1drop
250 mMTris-HCl1drop
3300 mM1dropNaCl
45 mMAdoMet1drop
5100 mMsodium citrate1reservoir
650 mMlithium sulfate1reservoir
716-18 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.98→10 Å / Num. all: 70596 / Num. obs: 27574 / % possible obs: 98 % / Rsym value: 0.049
Reflection
*PLUS
% possible obs: 98 % / Num. measured all: 70596 / Rmerge(I) obs: 0.049

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Processing

Software
NameClassification
DMmodel building
REFMACrefinement
MAR345data collection
SCALEPACKdata scaling
DMphasing
RefinementMethod to determine structure: MIR / Resolution: 1.98→10 Å /
RfactorNum. reflection
Rfree0.236 1411
Rwork0.205 -
Refinement stepCycle: LAST / Resolution: 1.98→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2002 0 27 165 2194
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.1
X-RAY DIFFRACTIONp_angle_d0.02
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / Rfactor obs: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.1
X-RAY DIFFRACTIONp_angle_d0.02

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