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

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Basic information

Entry
Database: PDB / ID: 4yqr
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 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
Chem-4HQ / tRNA (guanine-N(1)-)-methyltransferase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.701 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)28,5962
Polymers28,3851
Non-polymers2111
Water3,027168
1
A: tRNA (guanine-N(1)-)-methyltransferase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)57,1924
Polymers56,7692
Non-polymers4222
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area7020 Å2
ΔGint-27 kcal/mol
Surface area20800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.864, 93.864, 178.490
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-538-

HOH

21A-558-

HOH

31A-561-

HOH

41A-566-

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-4HQ / (4-amino-1,2,5-oxadiazol-3-yl)(4-methylpiperazin-1-yl)methanone


Mass: 211.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H13N5O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 53.86 %
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 10, 2010
RadiationMonochromator: unknown / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.66→50 Å / Num. obs: 35819 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.061 / Χ2: 1.055 / Net I/av σ(I): 30.626 / Net I/σ(I): 9.8 / Num. measured all: 251354
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.66-1.7270.54635241.01299.7
1.72-1.7970.41535691.07699.8
1.79-1.877.10.2835471.05499.8
1.87-1.977.10.18635191.07199.9
1.97-2.097.10.1335611.05799.9
2.09-2.257.10.09435611.023100
2.25-2.487.10.0835841.072100
2.48-2.8470.07935981.035100
2.84-3.586.90.06136061.068100
3.58-506.80.03237501.08599.8

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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: 1.701→29.051 Å / FOM work R set: 0.8772 / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1954 2000 5.97 %Random selection
Rwork0.164 31485 --
obs0.1659 33485 99.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.47 Å2 / Biso mean: 29.24 Å2 / Biso min: 12.76 Å2
Refinement stepCycle: final / Resolution: 1.701→29.051 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1874 0 28 168 2070
Biso mean--28.58 37.48 -
Num. residues----241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121963
X-RAY DIFFRACTIONf_angle_d1.3192666
X-RAY DIFFRACTIONf_chiral_restr0.065296
X-RAY DIFFRACTIONf_plane_restr0.007351
X-RAY DIFFRACTIONf_dihedral_angle_d12.533749
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7006-1.74310.26481410.21182227236899
1.7431-1.79020.21991420.187722192361100
1.7902-1.84290.22381410.175622292370100
1.8429-1.90240.21611410.165822212362100
1.9024-1.97040.20271410.172922142355100
1.9704-2.04920.19751430.168122442387100
2.0492-2.14250.20681410.167322392380100
2.1425-2.25540.21681420.162122292371100
2.2554-2.39660.20221420.169322402382100
2.3966-2.58160.2191440.178422612405100
2.5816-2.84120.20331440.175322702414100
2.8412-3.25180.20251430.170422592402100
3.2518-4.09510.16831460.144522892435100
4.0951-29.05510.17481490.15522344249399
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)
10.7464-0.3484-0.58911.05530.38423.26150.01580.0072-0.0284-0.0999-0.0120.1168-0.0238-0.2732-0.00640.106-0.0235-0.02230.137-0.00950.1464-24.045231.5196-11.348
22.6924-1.1949-0.73215.0835-1.12032.5613-0.1752-0.133-0.1557-0.00710.33640.4155-0.258-0.5025-0.01020.16290.03640.00040.20430.00760.1961-29.790738.996622.1857
33.3909-0.37611.52985.8382-3.95958.1962-0.0451-0.7081-0.26110.29220.25950.68170.1862-0.1823-0.12250.1740.09710.05210.32420.05190.272-38.914742.126725.9359
46.65111.3722-1.21483.51370.75365.01710.0201-0.31050.4027-0.0986-0.06270.2688-0.3814-0.17480.03810.17090.0536-0.03410.18560.00620.2127-39.116653.271816.718
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid -1:159)A-1 - 159
2X-RAY DIFFRACTION2(chain A and resid 160:192)A160 - 192
3X-RAY DIFFRACTION3(chain A and resid 193:214)A193 - 214
4X-RAY DIFFRACTION4(chain A and resid 215:246)A215 - 246

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