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

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Basic information

Entry
Database: PDB / ID: 4ypz
TitleCrystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds
ComponentstRNA (guanine-N(1)-)-methyltransferase
Keywordstransferase/transferase inhibitor / TrmD / Haemophilus influenzae / Dimerization / SAM-binding / knot / transferase-transferase inhibitor complex
Function / homology
Function and homology information


tRNA N1-guanine methylation / tRNA (guanine37-N1)-methyltransferase / tRNA (guanine(37)-N1)-methyltransferase activity / 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
4-(1H-imidazol-2-yl)pyridine / tRNA (guanine-N(1)-)-methyltransferase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,5302
Polymers28,3851
Non-polymers1451
Water2,468137
1
A: tRNA (guanine-N(1)-)-methyltransferase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)57,0594
Polymers56,7692
Non-polymers2902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area6740 Å2
ΔGint-23 kcal/mol
Surface area20930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.773, 93.773, 179.162
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-497-

HOH

21A-529-

HOH

31A-535-

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-4FL / 4-(1H-imidazol-2-yl)pyridine


Mass: 145.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H7N3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.67 Å3/Da / Density % sol: 53.94 %
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 4, 2010
RadiationMonochromator: unknown / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.71→50 Å / Num. obs: 33022 / % possible obs: 99.9 % / Redundancy: 8.3 % / Biso Wilson estimate: 26.73 Å2 / Rmerge(I) obs: 0.054 / Χ2: 1.056 / Net I/av σ(I): 32.949 / Net I/σ(I): 12.1 / Num. measured all: 272728
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.71-1.777.80.56932711.091100
1.77-1.848.40.43432531.074100
1.84-1.938.40.28632751.078100
1.93-2.038.40.19432811.03100
2.03-2.158.40.14432681.055100
2.15-2.328.40.12232861.028100
2.32-2.558.40.09332921.069100
2.55-2.928.40.06733201.041100
2.92-3.688.30.05233391.068100
3.68-507.90.0334371.02899.3

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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: 1.84→30.083 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1943 1609 6.06 %Random selection
Rwork0.1671 24963 --
obs0.1687 26572 99.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.82 Å2 / Biso mean: 33.2773 Å2 / Biso min: 14.99 Å2
Refinement stepCycle: final / Resolution: 1.84→30.083 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1835 0 11 137 1983
Biso mean--30.48 38.89 -
Num. residues----236
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061950
X-RAY DIFFRACTIONf_angle_d1.0032654
X-RAY DIFFRACTIONf_chiral_restr0.043297
X-RAY DIFFRACTIONf_plane_restr0.004353
X-RAY DIFFRACTIONf_dihedral_angle_d13.128757
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 (%)
1.84-1.89940.25721430.191522222365100
1.8994-1.96730.22871450.171322492394100
1.9673-2.0460.19891450.169722492394100
2.046-2.13910.22081450.166922522397100
2.1391-2.25190.20071460.163622522398100
2.2519-2.39290.23511440.178222452389100
2.3929-2.57760.22381460.176322652411100
2.5776-2.83680.20851470.183622722419100
2.8368-3.24690.19351470.1822942441100
3.2469-4.08910.17711480.154622992447100
4.0891-30.08720.16491530.1572364251799
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)
13.8511.4061-1.39552.8351-1.90797.1143-0.12160.041-0.39330.0020.08520.19210.5155-0.5520.04460.1715-0.02630.02130.1442-0.01860.2003-25.298322.8406-2.9654
22.3008-1.4113-2.04172.41581.10414.67710.07880.0470.077-0.2122-0.00930.0994-0.3065-0.2474-0.0650.1786-0.0054-0.04640.1599-0.01810.1567-23.446233.913-16.8778
35.17611.1743-0.5224.3406-0.11243.99060.06030.00860.01950.1936-0.07260.2837-0.2006-0.2739-0.01280.16190.0294-0.01540.1821-0.0130.1398-26.327734.0479-1.4654
46.0964-3.872.14534.6568-2.13042.5937-0.1947-0.7219-0.29380.24930.45390.6048-0.1445-0.5651-0.22460.26770.07320.04050.34690.04420.265-33.219939.768826.9014
55.23582.4157-3.33475.3912-1.04648.1948-0.1095-0.36530.40050.02050.04910.2714-0.3793-0.06880.0540.18390.0758-0.04830.2552-0.02320.26-38.418352.255917.1979
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid -1:34)A-1 - 34
2X-RAY DIFFRACTION2(chain A and resid 35:132)A35 - 132
3X-RAY DIFFRACTION3(chain A and resid 133:160)A133 - 160
4X-RAY DIFFRACTION4(chain A and resid 173:209)A173 - 209
5X-RAY DIFFRACTION5(chain A and resid 210:246)A210 - 246

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