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- PDB-4cng: Crystal structure of Sulfolobus acidocaldarius TrmJ in complex wi... -

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Basic information

Entry
Database: PDB / ID: 4cng
TitleCrystal structure of Sulfolobus acidocaldarius TrmJ in complex with S-adenosyl-L-Homocysteine
ComponentsSPOU RRNA METHYLASE
KeywordsTRANSFERASE / TRNA 2'-O-METHYLTRANSFERASE / SPOUT
Function / homology
Function and homology information


tRNA (cytidine(32)/uridine(32)-2'-O)-methyltransferase activity / tRNA nucleoside ribose methylation / Transferases; Transferring one-carbon groups; Methyltransferases / RNA binding / cytosol
Similarity search - Function
: / RNA methyltransferase TrmJ/LasT / tRNA/rRNA methyltransferase, SpoU type / SpoU rRNA Methylase family / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / tRNA (cytidine-2'-O-)-methyltransferase TrmJ
Similarity search - Component
Biological speciesSULFOLOBUS ACIDOCALDARIUS (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsVan Laer, B. / Somme, J. / Roovers, M. / Steyaert, J. / Droogmans, L. / Versees, W.
CitationJournal: RNA / Year: 2014
Title: Characterization of Two Homologous 2'-O-Methyltransferases Showing Different Specificities for Their tRNA Substrates.
Authors: Somme, J. / Van Laer, B. / Roovers, M. / Steyaert, J. / Versees, W. / Droogmans, L.
History
DepositionJan 22, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_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: SPOU RRNA METHYLASE
B: SPOU RRNA METHYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4076
Polymers58,1622
Non-polymers1,2454
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-14.9 kcal/mol
Surface area12960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.803, 54.097, 130.637
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein SPOU RRNA METHYLASE / TRNA METHYLTRANSFERASE / TRMJ


Mass: 29080.924 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: TRNA CM32 METHYLTRANSFERASE
Source: (gene. exp.) SULFOLOBUS ACIDOCALDARIUS (acidophilic)
Strain: ATCC33909 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS
References: UniProt: Q4JB16, tRNA (cytidine32/uridine32-2'-O)-methyltransferase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.27 Å3/Da / Density % sol: 45.85 % / Description: NONE
Crystal growpH: 5.5 / Details: 0.2M KBR, 0.1 M NA-ACETATE PH 5.5, 20% PEG2000MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9763
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.1→43 Å / Num. obs: 128921 / % possible obs: 97.5 % / Observed criterion σ(I): 1.2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.5
Reflection shellResolution: 1.1→1.2 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.94 / Mean I/σ(I) obs: 1.2 / % possible all: 93.3

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CNF

4cnf


Resolution: 1.1→43.26 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.97 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.18458 6470 5 %RANDOM
Rwork0.16156 ---
obs0.16273 122349 97.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.344 Å2
Baniso -1Baniso -2Baniso -3
1--1.02 Å20 Å20 Å2
2--0.72 Å20 Å2
3---0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.1→43.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2433 0 84 89 2606
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192628
X-RAY DIFFRACTIONr_bond_other_d00.022607
X-RAY DIFFRACTIONr_angle_refined_deg1.5472.0163565
X-RAY DIFFRACTIONr_angle_other_deg3.51536003
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1935315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.41424.018112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.8315475
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1751518
X-RAY DIFFRACTIONr_chiral_restr0.1330.2415
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212871
X-RAY DIFFRACTIONr_gen_planes_other0.0380.02565
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_it9.891.7091257
X-RAY DIFFRACTIONr_mcbond_other9.8951.711256
X-RAY DIFFRACTIONr_mcangle_it12.1342.5331573
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it14.2172.5451370
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_restr19.32935234
X-RAY DIFFRACTIONr_sphericity_free34.354532
X-RAY DIFFRACTIONr_sphericity_bonded26.0855238
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 440 -
Rwork0.343 8383 -
obs--91.08 %

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