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

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Basic information

Entry
Database: PDB / ID: 4yqs
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-4H9 / tRNA (guanine-N(1)-)-methyltransferase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.902 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. / 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)28,6032
Polymers28,3851
Non-polymers2181
Water2,918162
1
A: tRNA (guanine-N(1)-)-methyltransferase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)57,2064
Polymers56,7692
Non-polymers4362
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area6700 Å2
ΔGint-24 kcal/mol
Surface area20970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.353, 94.353, 177.775
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-525-

HOH

21A-552-

HOH

31A-557-

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-4H9 / (5-amino-1H-1,2,4-triazol-1-yl)(4-methoxyphenyl)methanone


Mass: 218.212 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10N4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.68 Å3/Da / Density % sol: 54.15 %
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-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 22, 2009
RadiationMonochromator: unknown / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 24218 / % possible obs: 99.9 % / Redundancy: 9.3 % / Biso Wilson estimate: 24.08 Å2 / Rmerge(I) obs: 0.074 / Χ2: 1.04 / Net I/av σ(I): 28.022 / Net I/σ(I): 11.3 / Num. measured all: 224381
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.9-1.979.20.53323921.018100
1.97-2.059.30.3723851.045100
2.05-2.149.30.25424001.038100
2.14-2.259.30.18824061.052100
2.25-2.399.40.14723891.06100
2.39-2.589.40.10724101.03299.9
2.58-2.849.30.07924151.002100
2.84-3.259.30.07124361.024100
3.25-4.099.20.0624601.027100
4.09-508.90.03425251.10299.3

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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: 1.902→37.122 Å / FOM work R set: 0.8838 / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1849 1269 5.24 %Random selection
Rwork0.1591 22947 --
obs0.1605 24216 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.94 Å2 / Biso mean: 27.99 Å2 / Biso min: 11.18 Å2
Refinement stepCycle: final / Resolution: 1.902→37.122 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1832 0 26 162 2020
Biso mean--32.23 36.51 -
Num. residues----237
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0181915
X-RAY DIFFRACTIONf_angle_d1.6762599
X-RAY DIFFRACTIONf_chiral_restr0.108289
X-RAY DIFFRACTIONf_plane_restr0.009340
X-RAY DIFFRACTIONf_dihedral_angle_d12.478719
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9022-1.97830.23851440.193725142658100
1.9783-2.06840.2031450.166225172662100
2.0684-2.17740.21141450.150525142659100
2.1774-2.31380.18191320.143825202652100
2.3138-2.49240.19441410.156625382679100
2.4924-2.74320.19631310.153425432674100
2.7432-3.13990.21531450.167625572702100
3.1399-3.95520.16421410.153525872728100
3.9552-37.12950.16391450.1622657280299
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)
10.6403-0.3088-0.40271.23990.35332.58380.01120.0152-0.009-0.0999-0.01870.116-0.0664-0.2447-0.00530.1188-0.0254-0.02270.1506-0.01150.1492-24.170131.8053-11.231
23.3492-2.56910.52134.072-0.98411.5891-0.0469-0.14220.015-0.02060.0950.2609-0.0794-0.149-0.03740.15280.024-0.00740.2101-0.0090.1902-36.251246.600821.5732
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid -1:161)A-1 - 161
2X-RAY DIFFRACTION2(chain A and resid 173:246)A173 - 246

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