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- PDB-5kzk: Crystal Structure of rRNA methyltransferase from Sinorhizobium me... -

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Basic information

Entry
Database: PDB / ID: 5kzk
TitleCrystal Structure of rRNA methyltransferase from Sinorhizobium meliloti
ComponentsProbable RNA methyltransferase, TrmH family
KeywordsRNA BINDING PROTEIN / SPOUT Methyltransferase / rRNA methylation / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC
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
: / Probable RNA methyltransferase, TrmH family
Similarity search - Component
Biological speciesRhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.28 Å
AuthorsDey, D. / Hegde, R.P. / Almo, S.C. / Ramakumar, S. / Ramagopal, U.A. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To Be Published
Title: Crystal Structure of rRNA methyltransferase from Sinorhizobium meliloti
Authors: Dey, D. / Hegde, R.P. / Almo, S.C. / Ramakumar, S. / Ramagopal, U.A.
History
DepositionJul 25, 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 1.2Nov 20, 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_comp_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_comp_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_comp_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_comp_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.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)63,4416
Polymers63,1312
Non-polymers3104
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-56 kcal/mol
Surface area23170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.820, 84.302, 112.045
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.: 2 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.11 %
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: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.987 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.28→67.36 Å / Num. obs: 28693 / % possible obs: 98 % / Redundancy: 7.9 % / CC1/2: 0.919 / Net I/σ(I): 46.98

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Processing

Software
NameVersionClassification
HKL-3000data processing
SHELXDEphasing
REFMAC5.8.0103refinement
RefinementMethod to determine structure: SAD / Resolution: 2.28→67.36 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.891 / SU B: 14.659 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.293 / ESU R Free: 0.234
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25863 1386 4.9 %RANDOM
Rwork0.20615 ---
obs0.20867 26732 96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å2-0 Å20 Å2
2--1.21 Å20 Å2
3----0.82 Å2
Refinement stepCycle: 1 / Resolution: 2.28→67.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3917 0 12 37 3966
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0193996
X-RAY DIFFRACTIONr_bond_other_d0.0020.023961
X-RAY DIFFRACTIONr_angle_refined_deg2.0751.9795434
X-RAY DIFFRACTIONr_angle_other_deg1.12339041
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.365520
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.22523.333159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.23515637
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1651536
X-RAY DIFFRACTIONr_chiral_restr0.1160.2663
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214509
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02867
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_it2.0842.6732086
X-RAY DIFFRACTIONr_mcbond_other2.0822.6732085
X-RAY DIFFRACTIONr_mcangle_it3.5193.9912601
X-RAY DIFFRACTIONr_mcangle_other3.5193.9912602
X-RAY DIFFRACTIONr_scbond_it2.4982.9231910
X-RAY DIFFRACTIONr_scbond_other2.4832.9191902
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1124.2632821
X-RAY DIFFRACTIONr_long_range_B_refined5.71720.374166
X-RAY DIFFRACTIONr_long_range_B_other5.71720.3774165
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.275→2.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 82 -
Rwork0.263 1572 -
obs--78.09 %
Refinement TLS params.Method: refined / Origin x: 35.37 Å / Origin y: 44.632 Å / Origin z: 8.874 Å
111213212223313233
T0.0766 Å2-0.0335 Å2-0.0299 Å2-0.0245 Å20.0016 Å2--0.1516 Å2
L0.8302 °20.2003 °2-0.2072 °2-0.2421 °20.1059 °2--0.4693 °2
S-0.0858 Å °0.1053 Å °-0.082 Å °0.0014 Å °0.0379 Å °0.0423 Å °-0.0733 Å °0.037 Å °0.0478 Å °

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