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- PDB-4yq8: Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SA... -

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Basic information

Entry
Database: PDB / ID: 4yq8
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 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
Chem-4FV / tRNA (guanine-N(1)-)-methyltransferase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsElkins, P.A. / Bonnette, W.G. / Madauss, K.P. / 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.
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)28,5972
Polymers28,3851
Non-polymers2121
Water2,666148
1
A: tRNA (guanine-N(1)-)-methyltransferase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)57,1944
Polymers56,7692
Non-polymers4242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area7020 Å2
ΔGint-27 kcal/mol
Surface area21080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.605, 93.605, 177.916
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-509-

HOH

21A-541-

HOH

31A-543-

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-4FV / 4-amino-N-[(1R,3S)-3-hydroxycyclopentyl]-1,2,5-oxadiazole-3-carboxamide


Mass: 212.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H12N4O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.64 Å3/Da / Density % sol: 53.45 %
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: Mar 13, 2010
RadiationMonochromator: unknown / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 27963 / % possible obs: 99.6 % / Redundancy: 6.5 % / Biso Wilson estimate: 26.84 Å2 / Rmerge(I) obs: 0.056 / Χ2: 1.054 / Net I/av σ(I): 28.296 / Net I/σ(I): 11.7 / Num. measured all: 180765
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.8-1.866.50.65527521.02299.1
1.86-1.946.50.4427371.05699.2
1.94-2.036.50.29327631.0999.4
2.03-2.136.50.19427791.08399.5
2.13-2.276.50.14527601.07999.6
2.27-2.446.50.11327811.06199.7
2.44-2.696.50.07528091.04299.8
2.69-3.086.50.06128181.02699.9
3.08-3.886.50.0428361.02299.9
3.88-306.20.03129281.05899.4

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Processing

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

1p9p


Resolution: 1.94→29.959 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2019 1605 7.15 %Random selection
Rwork0.1646 20850 --
obs0.1672 22455 99.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.26 Å2 / Biso mean: 32.5068 Å2 / Biso min: 15.06 Å2
Refinement stepCycle: final / Resolution: 1.94→29.959 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1879 0 27 148 2054
Biso mean--35.53 38.22 -
Num. residues----242
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041959
X-RAY DIFFRACTIONf_angle_d0.762654
X-RAY DIFFRACTIONf_chiral_restr0.03292
X-RAY DIFFRACTIONf_plane_restr0.004351
X-RAY DIFFRACTIONf_dihedral_angle_d12.008745
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 (%)
1.94-2.00260.21771450.1671884202999
2.0026-2.07420.22451420.16421848199099
2.0742-2.15720.20581440.15818632007100
2.1572-2.25530.20691440.156418762020100
2.2553-2.37420.17921450.164118832028100
2.3742-2.52290.19981440.17418752019100
2.5229-2.71760.2041470.168819022049100
2.7176-2.99080.21541460.180718912037100
2.9908-3.4230.2081460.173119032049100
3.423-4.31060.19031480.150619312079100
4.3106-29.96250.20131540.16491994214899
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)
10.565-0.4773-0.22861.13480.47552.23120.0125-0.001-0.0299-0.095-0.03190.1247-0.0292-0.22630.02450.1747-0.0213-0.02220.2066-0.0120.2113-24.020631.3015-11.1856
21.335-1.0765-0.05082.4058-1.06891.0584-0.1068-0.2116-0.09760.08690.26930.3429-0.0013-0.1923-0.15440.22970.0519-0.00920.31010.01350.2834-33.652943.128922.336
33.52620.57221.1032.82861.03995.45080.023-0.06410.2465-0.06880.21920.0243-0.4149-0.1618-0.23480.25310.0487-0.01240.3357-0.04170.3745-42.396753.461317.9081
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid -2:161)A-2 - 161
2X-RAY DIFFRACTION2(chain A and resid 169:223)A169 - 223
3X-RAY DIFFRACTION3(chain A and resid 224:245)A224 - 245

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