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- PDB-4yq1: Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SA... -

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Basic information

Entry
Database: PDB / ID: 4yq1
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-4FN / tRNA (guanine-N(1)-)-methyltransferase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsElkins, P.A. / Bonnette, W.G. / Madauss, K.P. / Stuckey, J.A.
CitationJournal: To be published
Title: To Be Published
Authors: Elkins, P.A. / Bonnette, W.G. / Madauss, K.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_prerelease_seq / 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)28,8182
Polymers28,3851
Non-polymers4341
Water1,51384
1
A: tRNA (guanine-N(1)-)-methyltransferase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)57,6364
Polymers56,7692
Non-polymers8672
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z1
Buried area7270 Å2
ΔGint-20 kcal/mol
Surface area23040 Å2
MethodPISA
2
A: tRNA (guanine-N(1)-)-methyltransferase
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)86,4546
Polymers85,1543
Non-polymers1,3013
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area5010 Å2
ΔGint-26 kcal/mol
Surface area40460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.466, 97.466, 176.697
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-451-

HOH

21A-484-

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-4FN / N-(1-{[(3-tert-butylbenzoyl)amino]methyl}cyclohexyl)-2,1-benzoxazole-4-carboxamide


Mass: 433.543 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H31N3O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.85 Å3/Da / Density % sol: 56.77 %
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 300 mm CCD / Detector: CCD / Date: Nov 4, 2009
RadiationMonochromator: unknown / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 22253 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 28.72 Å2 / Rmerge(I) obs: 0.077 / Χ2: 0.927 / Net I/av σ(I): 6.862 / Net I/σ(I): 12.2 / Num. measured all: 163780
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2-2.077.30.63421851.03100
2.07-2.157.40.46221941.046100
2.15-2.257.40.34422181.044100
2.25-2.377.40.24821911.042100
2.37-2.527.50.18222061.021100
2.52-2.717.50.12822291.021100
2.71-2.997.40.122110.982100
2.99-3.427.40.08122381.03100
3.42-4.317.30.05322570.05100
4.31-506.90.03423241.01399.1

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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: 2→31.396 Å / FOM work R set: 0.8522 / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2173 1999 8.99 %Random selection
Rwork0.1893 20236 --
obs0.1918 22235 99.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.96 Å2 / Biso mean: 35.81 Å2 / Biso min: 14.93 Å2
Refinement stepCycle: final / Resolution: 2→31.396 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1911 0 32 84 2027
Biso mean--27.29 38.65 -
Num. residues----244
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082024
X-RAY DIFFRACTIONf_angle_d1.1272748
X-RAY DIFFRACTIONf_chiral_restr0.043299
X-RAY DIFFRACTIONf_plane_restr0.005375
X-RAY DIFFRACTIONf_dihedral_angle_d13.732790
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 (%)
1.9948-2.04470.2391380.21691389152798
2.0447-2.10.25251400.210814221562100
2.1-2.16180.26811420.199814471589100
2.1618-2.23150.22821400.188714231563100
2.2315-2.31130.23331430.18314371580100
2.3113-2.40380.21421410.186614381579100
2.4038-2.51310.24781420.184614301572100
2.5131-2.64550.20671420.191114421584100
2.6455-2.81120.24191430.198314511594100
2.8112-3.02810.24951440.205314501594100
3.0281-3.33250.21871430.186914441587100
3.3325-3.8140.19711440.18114601604100
3.814-4.80250.20291470.173414781625100
4.8025-31.39950.19471500.19571525167599
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)
10.9565-0.1897-0.36071.08610.11112.3429-0.0593-0.0307-0.14640.1750.04520.09410.0767-0.09290.03330.18260.01740.02780.13790.0420.159537.5443-4.544111.7415
22.0424-1.73540.75695.68241.02413.9798-0.03520.05690.3879-0.18590.0035-0.5740.03310.4853-0.03140.25030.06380.07110.357-0.02290.410662.4618-10.8647-14.7873
33.0512-1.32551.48134.2744-0.30440.81320.0620.1192-0.2444-0.35810.0878-0.19010.03870.2216-0.0770.39560.03110.04890.2988-0.01170.235449.7095-13.0297-24.6864
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid -7:161)A-7 - 161
2X-RAY DIFFRACTION2(chain A and resid 210:246)A210 - 246
3X-RAY DIFFRACTION3(chain A and resid 171:209)A171 - 209

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