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- PDB-5a7t: Crystal structure of Sulfolobus acidocaldarius Trm10 at 2.4 angst... -

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Basic information

Entry
Database: PDB / ID: 5a7t
TitleCrystal structure of Sulfolobus acidocaldarius Trm10 at 2.4 angstrom resolution.
ComponentsTRNA (ADENINE(9)-N1)-METHYLTRANSFERASE
KeywordsTRANSFERASE / SPOUT / TRM10 / TRNA METHYLTRANSFERASE
Function / homology
Function and homology information


tRNA (adenine9-N1)-methyltransferase / tRNA (adenine(9)-N1)-methyltransferase activity / tRNA methylation / tRNA processing / cytoplasm
Similarity search - Function
: / tRNA methyltransferase, archaea / tRNA methyltransferase TRM10-type domain / tRNA methyltransferase TRM10-type domain superfamily / SAM-dependent methyltransferase TRM10-type domain profile.
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / tRNA (adenine(9)-N1)-methyltransferase
Similarity search - Component
Biological speciesSULFOLOBUS ACIDOCALDARIUS (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsVan Laer, B. / Roovers, M. / Wauters, L. / Kasprzak, J. / Dyzma, M. / Deyaert, E. / Feller, A. / Bujnicki, J. / Droogmans, L. / Versees, W.
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Structural and Functional Insights Into tRNA Binding and Adenosine N1-Methylation by an Archaeal Trm10 Homologue.
Authors: Van Laer, B. / Roovers, M. / Wauters, L. / Kasprzak, J.M. / Dyzma, M. / Deyaert, E. / Kumar Singh, R. / Feller, A. / Bujnicki, J.M. / Droogmans, L. / Versees, W.
History
DepositionJul 9, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2016Group: Database references
Revision 1.2Aug 23, 2017Group: Data collection / Refinement description / Category: diffrn_detector / software / Item: _diffrn_detector.type / _software.name
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _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: TRNA (ADENINE(9)-N1)-METHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6412
Polymers30,5351
Non-polymers1061
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.730, 46.400, 139.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TRNA (ADENINE(9)-N1)-METHYLTRANSFERASE / TRNA(M1A9)-METHYLTRANSFERASE / TRNA(M1A9)MTASE / TRM10


Mass: 30534.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS ACIDOCALDARIUS (acidophilic)
Plasmid: PET28B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS
References: UniProt: Q4J894, tRNA (adenine9-N1)-methyltransferase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 7.5
Details: 8 % ETHYLENE GLYCOL, 0.1 M HEPES PH 7.5, 10 % PEG8K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97918
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.4→44 Å / Num. obs: 11139 / % possible obs: 99.9 % / Observed criterion σ(I): 1.5 / Redundancy: 7.7 % / Rmerge(I) obs: 0.01 / Net I/σ(I): 10.16
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 4.17 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 1.74 / % possible all: 99.9

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
SHELXDEphasing
autoSHARPphasing
REFMAC5.8.0069refinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.4→44.01 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.924 / Cross valid method: THROUGHOUT / ESU R: 0.406 / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25001 557 5 %RANDOM
Rwork0.1789 ---
obs0.18239 10581 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.09 Å2
Baniso -1Baniso -2Baniso -3
1-2.13 Å20 Å20 Å2
2---0.88 Å20 Å2
3----1.25 Å2
Refinement stepCycle: LAST / Resolution: 2.4→44.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2006 0 7 30 2043
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192048
X-RAY DIFFRACTIONr_bond_other_d00.022085
X-RAY DIFFRACTIONr_angle_refined_deg1.4252.0022754
X-RAY DIFFRACTIONr_angle_other_deg3.48134795
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2945253
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.57823.70889
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.26615389
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9151518
X-RAY DIFFRACTIONr_chiral_restr0.0780.2320
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022252
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02440
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_it3.0574.0781015
X-RAY DIFFRACTIONr_mcbond_other3.0534.0741014
X-RAY DIFFRACTIONr_mcangle_it4.7436.1071267
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.0054.6181033
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 40 -
Rwork0.276 770 -
obs--100 %

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