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- PDB-3quv: Crystal structure of a tRNA-guanine-N1-methyltransferase from Myc... -

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Basic information

Entry
Database: PDB / ID: 3quv
TitleCrystal structure of a tRNA-guanine-N1-methyltransferase from Mycobacterium abscessus
ComponentstRNA (guanine-N(1)-)-methyltransferase
KeywordsTRANSFERASE / SSSGCID / Seattle Structural Genomics Center for Infectious Disease / SSGCID / tRNA methyltransferase / trmD / S-adenosyl-methionine / S-adenosyl-homocysteine / SAM / SAH / chronic lung disease / protein knot / 3(1) trefoil knot / domain swap
Function / homology
Function and homology information


tRNA (guanine37-N1)-methyltransferase / tRNA (guanine(37)-N1)-methyltransferase activity / tRNA N1-guanine methylation / cytosol
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 TrmD / 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 TrmD / 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 speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Tuberculosis (Edinb) / Year: 2015
Title: Increasing the structural coverage of tuberculosis drug targets.
Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / ...Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / Gardberg, A.S. / Choi, R. / Hewitt, S.N. / Napuli, A.J. / Myers, J. / Barrett, L.K. / Zhang, Y. / Ferrell, M. / Mundt, E. / Thompkins, K. / Tran, N. / Lyons-Abbott, S. / Abramov, A. / Sekar, A. / Serbzhinskiy, D. / Lorimer, D. / Buchko, G.W. / Stacy, R. / Stewart, L.J. / Edwards, T.E. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionFeb 24, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Sep 13, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)53,4266
Polymers53,1782
Non-polymers2484
Water7,026390
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7730 Å2
ΔGint-6 kcal/mol
Surface area19560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.660, 79.080, 86.010
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: 26588.838 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium abscessus (bacteria) / Strain: DSM 44196 / Gene: MAB_3226c, trmD / References: UniProt: B1MDI3, EC: 2.1.1.31
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 390 / 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: 2.36 Å3/Da / Density % sol: 47.78 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MyabA.00937.a.A1 PW30232 at 24.4 mg/mL against JCSG + E1, 2 M ammonium sulfate, 0.1 M sodium cacodylate pH 6.5 with 20% ethylene glycol as a cryo-protectant, crystal tracking ID 219633e1, ...Details: MyabA.00937.a.A1 PW30232 at 24.4 mg/mL against JCSG + E1, 2 M ammonium sulfate, 0.1 M sodium cacodylate pH 6.5 with 20% ethylene glycol as a cryo-protectant, crystal tracking ID 219633e1, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 55952 / Num. obs: 55136 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 27.064 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 27.52
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
1.7-1.746.60.4953.78265824112401297.6
1.74-1.790.4074.6525686388097.7
1.79-1.840.3215.8625026378498.2
1.84-1.90.2367.9624483369998
1.9-1.960.18110.2823683358298.3
1.96-2.030.14112.8523107349898.3
2.03-2.110.11216.0622008333998.4
2.11-2.190.08820.0221504325798.6
2.19-2.290.07423.6120548312598.8
2.29-2.40.06127.8919721299998.7
2.4-2.530.05430.9818741285798.9
2.53-2.690.04536.1217702270499
2.69-2.870.03941.5416570255099.1
2.87-3.10.03248.6815428239199
3.1-3.40.02659.2414086220599.4
3.4-3.80.02169.0912712201499.3
3.8-4.390.01974.3911086180099.3
4.39-5.380.01877.039638153199.4
5.38-7.60.01973.717547120599.6
7.60.01578.62404170497.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 57.11 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å45.67 Å
Translation3 Å45.67 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
BOSdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3knu

3knu


Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.1892 / WRfactor Rwork: 0.1645 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8875 / SU B: 3.682 / SU ML: 0.056 / SU R Cruickshank DPI: 0.0957 / SU Rfree: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1975 2798 5.1 %RANDOM
Rwork0.1709 ---
obs0.1723 54992 98.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 49.68 Å2 / Biso mean: 21.637 Å2 / Biso min: 8.66 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å20 Å20 Å2
2---0.22 Å20 Å2
3---0.76 Å2
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3352 0 16 390 3758
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223522
X-RAY DIFFRACTIONr_angle_refined_deg1.4481.9674823
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4335463
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.65922.721147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.43715552
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1941534
X-RAY DIFFRACTIONr_chiral_restr0.1010.2548
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212701
X-RAY DIFFRACTIONr_mcbond_it0.9121.52227
X-RAY DIFFRACTIONr_mcangle_it1.62923614
X-RAY DIFFRACTIONr_scbond_it2.41931295
X-RAY DIFFRACTIONr_scangle_it3.9764.51195
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 202 -
Rwork0.232 3794 -
all-3996 -
obs--97.27 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8076-0.321-0.62010.14870.260.59370.00030.00150.0054-0.0170.01150.00420.0184-0.018-0.01180.0292-0.0111-0.00280.0192-0.00340.04315.308110.159424.6561
20.4327-0.1213-0.27210.13870.16350.36310.037-0.03350.0545-0.0686-0.003-0.0245-0.0433-0.0007-0.0340.04350.00080.00720.0142-0.01330.03922.716819.49421.7663
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 227
2X-RAY DIFFRACTION2B0 - 231

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