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- PDB-4h3z: Crystal structure of a symmetric dimer of a tRNA (guanine-(N(1)-)... -

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Basic information

Entry
Database: PDB / ID: 4h3z
TitleCrystal structure of a symmetric dimer of a tRNA (guanine-(N(1)-)-methyltransferase from Burkholderia phymatum bound to S-adenosyl homocystein in both half-sites
ComponentstRNA (guanine-N(1)-)-methyltransferase
KeywordsTRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / tRNA methylation / m1G37 methylation / SAH / SAM / food parasite
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 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)62,4186
Polymers61,5782
Non-polymers8404
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7530 Å2
ΔGint-49 kcal/mol
Surface area21530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.850, 188.090, 127.680
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.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.87 Å3/Da / Density % sol: 57.13 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: BuphA.00054.a.A1 PS01368 at 35 mg/mL with 3 mM SAH against CSHT screen condition E10, 0.2 M NaCl, 0.1 M NaOAc pH 4.6, 30% MPD, crystal tracking ID 236894e10, unique puck ID zeh2-4, VAPOR ...Details: BuphA.00054.a.A1 PS01368 at 35 mg/mL with 3 mM SAH against CSHT screen condition E10, 0.2 M NaCl, 0.1 M NaOAc pH 4.6, 30% MPD, crystal tracking ID 236894e10, unique puck ID zeh2-4, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 28, 2012 / Details: VariMax
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 39035 / Num. obs: 38958 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 38.914 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 18.35
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.15-2.210.4844.717784284599.8
2.21-2.270.4235.4318044278599.8
2.27-2.330.4035.5917628266499.9
2.33-2.40.3176.91175252643100
2.4-2.480.2897.4116841254099.9
2.48-2.570.2388.5716356245799.8
2.57-2.670.2079.69160882406100
2.67-2.780.16511.4815216227599.9
2.78-2.90.1313.4214791219999.8
2.9-3.040.10515.8714179211299.9
3.04-3.210.08119.5213554201499.8
3.21-3.40.06623.7412862191399.8
3.4-3.630.05330.9312040179599.8
3.63-3.930.04338.6511185169199.7
3.93-4.30.03941.6410142153199.4
4.3-4.810.03546.429268141099.8
4.81-5.550.03643.638411126199.8
5.55-6.80.03738.7470481068100
6.8-9.620.02847.345515855100
9.620.02359.31289849497.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4H3Y

4h3y


Resolution: 2.15→42.2 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 8.687 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.185 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1953 5 %RANDOM
Rwork0.1864 ---
obs0.1886 38957 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 98.33 Å2 / Biso mean: 38.0892 Å2 / Biso min: 10.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20 Å20 Å2
2---0.48 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.15→42.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3867 0 54 223 4144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194023
X-RAY DIFFRACTIONr_bond_other_d0.0010.023773
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.9775476
X-RAY DIFFRACTIONr_angle_other_deg0.79838620
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8555508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.53723.032188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.65715627
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3141543
X-RAY DIFFRACTIONr_chiral_restr0.0790.2607
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214612
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02929
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 148 -
Rwork0.215 2691 -
all-2839 -
obs--99.75 %
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)
10.1446-0.2625-0.10610.70350.13950.2720.10630.0515-0.0607-0.1899-0.14630.0493-0.0729-0.05680.040.09490.05-0.03610.0817-0.02220.0657-12.7689-29.6793-15.1554
20.4781-0.6568-0.01621.34720.42740.46820.0620.05960.0984-0.1301-0.0832-0.0572-0.0740.06240.02110.0374-0.01130.03090.0502-0.01040.0823-0.9233-27.0763-10.5595
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 254
2X-RAY DIFFRACTION1A301 - 302
3X-RAY DIFFRACTION2B-1 - 254
4X-RAY DIFFRACTION2A303
5X-RAY DIFFRACTION2B301

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