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

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Basic information

Entry
Database: PDB / ID: 4ypw
TitleCrystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds
ComponentstRNA (guanine-N(1)-)-methyltransferase
Keywordstransferase/transferase inhibitor / TrmD / Haemophilus influenzae / 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
6-(benzylamino)pyridine-3-carboxamide / tRNA (guanine-N(1)-)-methyltransferase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.311 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)28,6122
Polymers28,3851
Non-polymers2271
Water55831
1
A: tRNA (guanine-N(1)-)-methyltransferase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)57,2244
Polymers56,7692
Non-polymers4552
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area6820 Å2
ΔGint-24 kcal/mol
Surface area21520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.892, 92.892, 178.097
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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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-4FD / 6-(benzylamino)pyridine-3-carboxamide


Mass: 227.262 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H13N3O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.6 Å3/Da / Density % sol: 52.78 %
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: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 16, 2010
RadiationMonochromator: unknown / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 10317 / % possible obs: 76.8 % / Redundancy: 9.2 % / Biso Wilson estimate: 37.78 Å2 / Rmerge(I) obs: 0.054 / Χ2: 1.048 / Net I/av σ(I): 35.643 / Net I/σ(I): 17 / Num. measured all: 94715
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.3-2.383.50.2092381.01818.3
2.38-2.4840.2014451.00733.6
2.48-2.595.20.196541.06549
2.59-2.736.20.1839121.08268.9
2.73-2.98.10.18712561.08694.2
2.9-3.1210.60.14913231.064100
3.12-3.4410.90.07913491.034100
3.44-3.9310.90.0513451.037100
3.93-4.9510.90.03813651.049100
4.95-5010.20.03514301.0299.9

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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: 2.311→39.235 Å / FOM work R set: 0.7604 / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2477 1022 9.96 %Random selection
Rwork0.192 9239 --
obs0.1974 10261 77.3 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.79 Å2 / Biso mean: 43.82 Å2 / Biso min: 12.82 Å2
Refinement stepCycle: final / Resolution: 2.311→39.235 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1872 0 17 31 1920
Biso mean--44.31 34.64 -
Num. residues----238
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021936
X-RAY DIFFRACTIONf_angle_d0.562618
X-RAY DIFFRACTIONf_chiral_restr0.019285
X-RAY DIFFRACTIONf_plane_restr0.003345
X-RAY DIFFRACTIONf_dihedral_angle_d9.912729
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3113-2.43310.3353460.245642246825
2.4331-2.58550.3621840.24675383745
2.5855-2.78510.34111350.25181225136073
2.7851-3.06530.3031860.25491683186999
3.0653-3.50860.28741880.214816901878100
3.5086-4.41950.23751900.161717161906100
4.4195-39.24080.18551930.16581750194398
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)
10.0829-0.0823-0.05020.34320.44490.58330.01920.0469-0.0073-0.0391-0.0195-0.0118-0.0198-0.058900.1102-0.0263-0.01010.176-0.00360.1601-24.175731.0165-11.1076
20.07440.18810.07340.48290.18540.0711-0.2467-0.1263-0.121-0.03480.28970.2009-0.14850.1015-0.00450.18070.1079-0.01420.32390.01690.1872-33.507839.67726.6182
30.1945-0.0911-0.15270.168-0.00970.1993-0.1101-0.34540.5601-0.0570.1309-0.0093-0.5140.01210.00870.24310.0567-0.03140.3407-0.0120.3078-38.426352.300316.955
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A resid -2:161)A0
2X-RAY DIFFRACTION2(chain A and resid 173:209)A173 - 209
3X-RAY DIFFRACTION3(chain A and resid 210:246)A210 - 246

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