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- PDB-5l0z: Crystal Structure of AdoMet bound rRNA methyltransferase from Sin... -

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Basic information

Entry
Database: PDB / ID: 5l0z
TitleCrystal Structure of AdoMet bound rRNA methyltransferase from Sinorhizobium meliloti
ComponentsProbable RNA methyltransferase, TrmH family
KeywordsTRANSFERASE / SPOUT Methyltransferase / AdoMet binding / Trefoil knot
Function / homology
Function and homology information


RNA methyltransferase activity / RNA processing / Transferases; Transferring one-carbon groups; Methyltransferases / methylation / RNA binding / cytoplasm
Similarity search - Function
RNA 2'-O ribose methyltransferase substrate binding / RNA 2-O ribose methyltransferase, substrate binding / : / MRM3-like substrate binding domain / RNA 2'-O ribose methyltransferase substrate binding / : / tRNA/rRNA methyltransferase, SpoU type / SpoU rRNA Methylase family / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot ...RNA 2'-O ribose methyltransferase substrate binding / RNA 2-O ribose methyltransferase, substrate binding / : / MRM3-like substrate binding domain / RNA 2'-O ribose methyltransferase substrate binding / : / 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 / 50S ribosomal protein L30e-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / S-ADENOSYLMETHIONINE / Probable RNA methyltransferase, TrmH family
Similarity search - Component
Biological speciesRhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsDey, D. / Hegde, R.P. / Almo, S.C. / Ramakumar, S. / Ramagopal, U.A.
CitationJournal: To Be Published
Title: Crystal Structure of AdoMet bound rRNA methyltransferase from Sinorhizobium meliloti
Authors: Dey, D. / Hegde, R.P. / Almo, S.C. / Ramakumar, S. / Ramagopal, U.A.
History
DepositionJul 28, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable RNA methyltransferase, TrmH family
B: Probable RNA methyltransferase, TrmH family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,35510
Polymers63,1312
Non-polymers1,2258
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-76 kcal/mol
Surface area22780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.855, 82.896, 108.806
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 Probable RNA methyltransferase, TrmH family


Mass: 31565.287 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium meliloti (strain 1021) (bacteria)
Strain: 1021 / Gene: SMc01130 / Plasmid: BC-pSGX4(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL
References: UniProt: Q92SJ4, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 46.98 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 5mM Cobalt chloride , 5mM Magnesium chloride hexahydrate, 0.1M HEPES pH 7.5, 9% wt/vol polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.542 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.9→65.94 Å / Num. obs: 13571 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.86 / Net I/σ(I): 28.51

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Processing

Software
NameVersionClassification
HKL-3000data processing
HKL-3000data scaling
REFMAC5.8.0155refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→65.94 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.862 / SU B: 39.924 / SU ML: 0.343 / Cross valid method: THROUGHOUT / ESU R Free: 0.451
Details: 1.542, HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26498 634 4.9 %RANDOM
Rwork0.19087 ---
obs0.19437 12403 96.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 56.424 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20 Å2-0 Å2
2---0.89 Å20 Å2
3---0.34 Å2
Refinement stepCycle: 1 / Resolution: 2.9→65.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3951 0 68 0 4019
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0194091
X-RAY DIFFRACTIONr_bond_other_d0.0020.024044
X-RAY DIFFRACTIONr_angle_refined_deg1.6671.9955566
X-RAY DIFFRACTIONr_angle_other_deg1.01539240
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5495523
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.89723.374163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.90715648
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7161537
X-RAY DIFFRACTIONr_chiral_restr0.0830.2677
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214594
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02893
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_it1.9574.3342104
X-RAY DIFFRACTIONr_mcbond_other1.9554.3342104
X-RAY DIFFRACTIONr_mcangle_it3.4046.4812623
X-RAY DIFFRACTIONr_mcangle_other3.4046.4832624
X-RAY DIFFRACTIONr_scbond_it2.0864.5761987
X-RAY DIFFRACTIONr_scbond_other2.0854.5761988
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4916.7822944
X-RAY DIFFRACTIONr_long_range_B_refined5.61652.2654343
X-RAY DIFFRACTIONr_long_range_B_other5.61552.264344
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 25 -
Rwork0.237 587 -
obs--62.26 %
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)
11.00910.0032-0.31460.5221-0.63760.9466-0.08010.1560.04560.00230.032-0.06580.01470.01310.04810.008-0.0267-0.010.18360.02490.11534.897844.87428.8879
21.37550.36070.18650.60130.10890.5767-0.10610.0453-0.06540.01810.08680.0531-0.0963-0.10020.01920.0329-0.00680.00580.16280.02120.092310.501139.490422.3585
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 284
2X-RAY DIFFRACTION2B16 - 283

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