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- PDB-4h3y: Crystal structure of an asymmetric dimer of a tRNA (guanine-(N(1)... -

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Basic information

Entry
Database: PDB / ID: 4h3y
TitleCrystal structure of an asymmetric dimer of a tRNA (guanine-(N(1)-)-methyltransferase from Burkholderia phymatum bound to S-adenosyl homocystein in one half-site
ComponentstRNA (guanine-N(1)-)-methyltransferase
KeywordsTRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / trmD / M1G-methyltransferase / G37 methyltransferase / S-adenosyl-methionine / SAM / S-adenosyl-homocysteine / SAH / tRNA modification / proteobacteria / nitrogen fixation / food pathogen / domain swapped homodimer
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
S-ADENOSYL-L-HOMOCYSTEINE / tRNA (guanine-N(1)-)-methyltransferase
Similarity search - Component
Biological speciesBurkholderia phymatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Plos One / Year: 2013
Title: Combining functional and structural genomics to sample the essential Burkholderia structome.
Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C.
History
DepositionSep 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Sep 20, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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


Theoretical massNumber of molelcules
Total (without water)61,9984
Polymers61,5782
Non-polymers4202
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7310 Å2
ΔGint-38 kcal/mol
Surface area22250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.970, 187.400, 127.640
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein tRNA (guanine-N(1)-)-methyltransferase / M1G-methyltransferase / tRNA [GM37] methyltransferase


Mass: 30788.926 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia phymatum (bacteria) / Strain: DSM 17167 STM815 / Gene: Bphy_0771, trmD / Production host: Escherichia coli (E. coli)
References: UniProt: B2JF31, tRNA (guanine37-N1)-methyltransferase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.86 Å3/Da / Density % sol: 57.04 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: BuphA.00054.a.A1 PS01368 at 35.3 mg/mL against JCSG II screen condition F12, 0.1 M phosphate-citrate pH 4.2, 5% PEG 3000, 25% 1,2 propanediol, 10% glycerol, crystal tracking ID 230666f12, ...Details: BuphA.00054.a.A1 PS01368 at 35.3 mg/mL against JCSG II screen condition F12, 0.1 M phosphate-citrate pH 4.2, 5% PEG 3000, 25% 1,2 propanediol, 10% glycerol, crystal tracking ID 230666f12, unique puck ID zjg9-5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 24981 / Num. obs: 24828 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 51.36 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 26.05
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.5-2.570.5444.1213749183899.6
2.57-2.640.4334.9713075175599.7
2.64-2.710.375.812737171199.4
2.71-2.80.2867.4312535168199.6
2.8-2.890.2319.1611980161399.8
2.89-2.990.17312.2311647157799.7
2.99-3.10.13815.0611115150799.7
3.1-3.230.10719.0510746146299.6
3.23-3.370.08223.2410271140899.8
3.37-3.540.06129.699755133999.9
3.54-3.730.04936.49308129999.9
3.73-3.950.04142.188752122299.8
3.95-4.230.03547.428094115099.7
4.23-4.560.0353.237505107199.4
4.56-50.0354.36683298699.6
5-5.590.03152.74618990099.6
5.59-6.460.0352.2539681399.6
6.46-7.910.02657.66458767999.1
7.91-11.180.01970.15369954599.6
11.180.01972.03170827281

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å19.87 Å
Translation3 Å19.87 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.1phasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3axz

3axz


Resolution: 2.5→19.87 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.932 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 14.88 / SU ML: 0.163 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.331 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2324 1266 5.1 %RANDOM
Rwork0.1813 ---
obs0.184 24828 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 122.47 Å2 / Biso mean: 49.7717 Å2 / Biso min: 20.89 Å2
Baniso -1Baniso -2Baniso -3
1-1.83 Å20 Å20 Å2
2---0.9 Å20 Å2
3----0.93 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3855 0 27 76 3958
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193968
X-RAY DIFFRACTIONr_bond_other_d0.0010.023702
X-RAY DIFFRACTIONr_angle_refined_deg1.4651.9685405
X-RAY DIFFRACTIONr_angle_other_deg0.8338443
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1175508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.87323.094181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.24215600
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2041540
X-RAY DIFFRACTIONr_chiral_restr0.0780.2604
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214589
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02919
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 101 -
Rwork0.272 1729 -
all-1830 -
obs--99.35 %
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)
10.0713-0.04260.03750.76650.01060.38530.0153-0.0439-0.0315-0.1545-0.07590.0877-0.037-0.09220.06060.05560.0402-0.040.081-0.01590.0495-13.2492-29.1594-15.598
20.345-0.46740.03291.09980.42650.5689-0.050.05060.0707-0.0670.0325-0.0195-0.14120.17540.01750.0598-0.0373-0.01150.0789-0.01740.0892-1.1377-26.9019-10.7956
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 254
2X-RAY DIFFRACTION2B0 - 254

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