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- PDB-3tm5: Crystal structure of Trm14 from Pyrococcus furiosus in complex wi... -

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Basic information

Entry
Database: PDB / ID: 3tm5
TitleCrystal structure of Trm14 from Pyrococcus furiosus in complex with sinefungin
ComponentsCrystal structure of Trm14
KeywordsTRANSFERASE / Rossmann fold / methyltransferase / THUMP domain / tRNA methyltransferase
Function / homology
Function and homology information


tRNA (guanine6-N2)-methyltransferase / tRNA (guanine(6)-N2)-methyltransferase activity / tRNA methylation / RNA binding / cytoplasm
Similarity search - Function
: / : / Uncharacterized protein family UPF0020 signature. / VC0802-like - #30 / Ribosomal RNA large subunit methyltransferase K/L-like, FLD domain / RMKL-like, methyltransferase domain / THUMP / THUMP domain / THUMP domain / THUMP domain profile. ...: / : / Uncharacterized protein family UPF0020 signature. / VC0802-like - #30 / Ribosomal RNA large subunit methyltransferase K/L-like, FLD domain / RMKL-like, methyltransferase domain / THUMP / THUMP domain / THUMP domain / THUMP domain profile. / VC0802-like / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
SINEFUNGIN / tRNA (guanine(6)-N2)-methyltransferase
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsFislage, M. / Roovers, M. / Tuszynska, I. / Bujnicki, J.M. / Droogmans, L. / Versees, W.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Crystal structures of the tRNA:m2G6 methyltransferase Trm14/TrmN from two domains of life.
Authors: Fislage, M. / Roovers, M. / Tuszynska, I. / Bujnicki, J.M. / Droogmans, L. / Versees, W.
History
DepositionAug 31, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1May 9, 2012Group: Other
Revision 1.2Oct 3, 2012Group: Database references
Revision 1.3Sep 13, 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

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Assembly

Deposited unit
A: Crystal structure of Trm14
B: Crystal structure of Trm14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,0264
Polymers84,2632
Non-polymers7632
Water4,558253
1
A: Crystal structure of Trm14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5132
Polymers42,1321
Non-polymers3811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Crystal structure of Trm14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5132
Polymers42,1321
Non-polymers3811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.245, 45.064, 121.082
Angle α, β, γ (deg.)90.00, 91.81, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe asymmetric unit contains two identical molecules connected by NCS

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Components

#1: Protein Crystal structure of Trm14


Mass: 42131.691 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: PF1002 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3)
References: UniProt: Q8U248, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N7O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.66 Å3/Da / Density % sol: 53.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100 mM Tris-acetate, 32% PEG 4000, 15% glycerol, crystal was soaked in crystallization solution containing 1 mM sinefungin, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 5, 2011
RadiationMonochromator: Bartels Monochromator with dual channel cut crystals (DCCM) in (+--+) geometry
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.834
11-h,-k,l20.166
ReflectionResolution: 2.27→50 Å / Num. all: 80676 / Num. obs: 55944 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.147 / Net I/σ(I): 8.6
Reflection shellResolution: 2.27→2.4 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.643 / Mean I/σ(I) obs: 2.08 / % possible all: 92.8

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3TLJ

3tlj


Resolution: 2.27→48.02 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.909 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21892 1908 5 %RANDOM
Rwork0.20397 ---
obs0.20474 36169 90.99 %-
all-43175 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.383 Å2
Baniso -1Baniso -2Baniso -3
1-9.15 Å20 Å21.85 Å2
2---6.02 Å20 Å2
3----3.12 Å2
Refine analyzeLuzzati coordinate error obs: 0.2756 Å
Refinement stepCycle: LAST / Resolution: 2.27→48.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5835 0 54 253 6142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0226016
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.611.9868101
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9045741
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.08223.702262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.771151141
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6011541
X-RAY DIFFRACTIONr_chiral_restr0.1110.2926
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024389
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.231.53662
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.11325899
X-RAY DIFFRACTIONr_scbond_it3.48332354
X-RAY DIFFRACTIONr_scangle_it5.284.52198
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.206→2.263 Å / Total num. of bins used: 20

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