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- PDB-4yqq: Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SA... -

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Basic information

Entry
Database: PDB / ID: 4yqq
TitleCrystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds
ComponentstRNA (guanine-N(1)-)-methyltransferase
Keywordstransferase/transferase inhibitor / TrmD / SAM-binding / knot / transferase-transferase inhibitor complex
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 / 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
Chem-4H7 / tRNA (guanine-N(1)-)-methyltransferase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsElkins, P.A. / Bonnette, W.G. / Stuckey, J.A.
CitationJournal: To Be Published
Title: Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds
Authors: Elkins, P.A. / Bonnette, W.G. / Williams, S.P. / Stuckey, J.A.
History
DepositionMar 13, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,7102
Polymers28,3851
Non-polymers3251
Water3,171176
1
A: tRNA (guanine-N(1)-)-methyltransferase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)57,4204
Polymers56,7692
Non-polymers6512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area6780 Å2
ΔGint-21 kcal/mol
Surface area20970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.390, 94.390, 178.917
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-477-

HOH

21A-491-

HOH

31A-493-

HOH

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Components

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


Mass: 28384.576 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) (bacteria)
Strain: ATCC 51907 / DSM 11121 / KW20 / Rd / Gene: trmD, HI_0202 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21*(DE3)pGro7
References: UniProt: P43912, tRNA (guanine37-N1)-methyltransferase
#2: Chemical ChemComp-4H7 / 6-{[2-(4-methylpiperazin-1-yl)benzyl]amino}pyridine-3-carboxamide


Mass: 325.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H23N5O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.7 Å3/Da / Density % sol: 54.48 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein solution:( 12/mg/mL in 100mM HEPES pH 7.5, 150mM NaCl, 10mM MgCl2 2mM DTT) Well solution: (20% PEG3,350 and 0.2M potassium citrate tribasic monohydrate). 4uL of S-adenosyl methionine ...Details: Protein solution:( 12/mg/mL in 100mM HEPES pH 7.5, 150mM NaCl, 10mM MgCl2 2mM DTT) Well solution: (20% PEG3,350 and 0.2M potassium citrate tribasic monohydrate). 4uL of S-adenosyl methionine in water were added to 100uL of protein and allowed to incubate on ice for 1 hour before protein was mixed with well at 1:1 ratio.Seeding used to improve crystals. Compound stock solutions (either 100mM or 1M stocks) were added up to a final drop concentration of 4.8% DMSO. Crystals were soaked for 4-6 hours. 20% glycerol in well solution was used as cryoprotectant for a quick dip of crystal in liquid N2.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 9, 2010
RadiationMonochromator: unknown / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.65→30 Å / Num. obs: 37102 / % possible obs: 99.8 % / Redundancy: 7.4 % / Biso Wilson estimate: 23.15 Å2 / Rmerge(I) obs: 0.051 / Χ2: 1.026 / Net I/av σ(I): 33.336 / Net I/σ(I): 12.3 / Num. measured all: 274827
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.65-1.717.40.70236611.02399.5
1.71-1.787.40.49736511.07499.6
1.78-1.867.40.3436751.01299.7
1.86-1.967.40.2136701.01599.8
1.96-2.087.40.14536981.05699.9
2.08-2.247.50.136831.0399.9
2.24-2.467.50.07137061.027100
2.46-2.827.50.06137221.011100
2.82-3.557.40.03837711.008100
3.55-307.20.02838651.00799.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P9P

1p9p


Resolution: 1.78→29.204 Å / FOM work R set: 0.8805 / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1964 1599 5.39 %Random selection
Rwork0.1627 28051 --
obs0.1645 29650 99.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.08 Å2 / Biso mean: 28.71 Å2 / Biso min: 12.79 Å2
Refinement stepCycle: final / Resolution: 1.78→29.204 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1841 0 47 176 2064
Biso mean--31.33 37.95 -
Num. residues----238
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071963
X-RAY DIFFRACTIONf_angle_d1.0252672
X-RAY DIFFRACTIONf_chiral_restr0.043294
X-RAY DIFFRACTIONf_plane_restr0.005360
X-RAY DIFFRACTIONf_dihedral_angle_d11.952765
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.78-1.83750.20461440.175525082652100
1.8375-1.90310.22431420.159925062648100
1.9031-1.97930.21440.163525282672100
1.9793-2.06940.20881440.156925242668100
2.0694-2.17840.1871450.156825382683100
2.1784-2.31490.19251430.160125212664100
2.3149-2.49350.23111460.172825552701100
2.4935-2.74430.20931450.170325492694100
2.7443-3.1410.21521460.180125662712100
3.141-3.95570.18061470.153325852732100
3.9557-29.20760.18071530.15792671282499
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)
11.04140.6293-0.43461.334-0.49012.4461-0.022-0.0142-0.190.00450.0480.11820.2482-0.2213-0.03580.2018-0.04490.01280.20880.01780.2137-25.423423.325-3.2804
21.1019-0.8097-0.86611.41170.63832.40870.04420.00040.0089-0.1494-0.00040.0064-0.1173-0.1079-0.03470.1696-0.0155-0.02170.1575-0.01370.1727-22.404433.7104-16.8736
30.8495-0.00790.34461.61220.0841.74980.0207-0.00190.0260.0006-0.01230.194-0.1579-0.34390.00170.15640.0075-0.0120.2115-0.01610.1894-27.848935.947-5.9122
42.073-1.29790.42842.1353-0.66330.554-0.1226-0.2240.00570.1070.19670.2263-0.0912-0.1931-0.06880.17750.03940.0060.2473-0.00820.2022-36.483946.449322.048
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid -2:34)A-2 - 34
2X-RAY DIFFRACTION2(chain A and resid 35:121)A35 - 121
3X-RAY DIFFRACTION3(chain A and resid 122:173)A122 - 173
4X-RAY DIFFRACTION4(chain A and resid 174:246)A174 - 246

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