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- PDB-3l8u: Crystal structure of SMU.1707c, a putative rRNA methyltransferase... -

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Basic information

Entry
Database: PDB / ID: 3l8u
TitleCrystal structure of SMU.1707c, a putative rRNA methyltransferase from streptococcus mutans UA159
ComponentsPutative rRNA methylase
KeywordsTRANSFERASE / streptococcus mutans / methyltransferase / knotted protein
Function / homology
Function and homology information


wobble position ribose methylation / tRNA (cytidine(34)-2'-O)-methyltransferase activity / tRNA (5-carboxymethylaminomethyluridine(34)-2'-O)-methyltransferase activity / tRNA (cytidine34-2'-O)-methyltransferase / RNA binding / identical protein binding / cytoplasm
Similarity search - Function
tRNA (cytidine/uridine-2'-O-)-methyltransferase / 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
Putative tRNA (cytidine(34)-2'-O)-methyltransferase
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGao, X.-Z. / Wang, K.-T. / Su, X.-D.
CitationJournal: To be published
Title: Crystal structure of SMU.1707c, a putative rRNA methyltransferase from streptococcus mutans UA159
Authors: Gao, X.-Z. / Wang, K.-T. / Su, X.-D.
History
DepositionJan 4, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 5, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative rRNA methylase
B: Putative rRNA methylase


Theoretical massNumber of molelcules
Total (without water)42,3802
Polymers42,3802
Non-polymers00
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-16 kcal/mol
Surface area15370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.277, 82.277, 70.992
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Putative rRNA methylase / SMU.1707c


Mass: 21190.129 Da / Num. of mol.: 2 / Mutation: M140V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: UA159 / Gene: SMU_1707c / Plasmid: pet28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DSR4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.83 Å3/Da / Density % sol: 56.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.5M (NH4)2SO4, 0.1M Bis-tris pH7.0, 0.7% beta-OG , VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Feb 22, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 31965 / Num. obs: 31772 / % possible obs: 99.3 % / Observed criterion σ(I): 1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3E5Y

3e5y


Resolution: 2→35.6 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.931 / Occupancy max: 1 / Occupancy min: 1 / SU B: 6.696 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23896 1604 5.1 %RANDOM
Rwork0.20603 ---
obs0.20763 30118 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 72.55 Å2 / Biso mean: 41.124 Å2 / Biso min: 22.97 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20 Å2
2---0.37 Å20 Å2
3---0.74 Å2
Refinement stepCycle: LAST / Resolution: 2→35.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2464 0 0 146 2610
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0212520
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6331.9363407
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7095302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.21924.198131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.0715423
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2111514
X-RAY DIFFRACTIONr_chiral_restr0.2640.2373
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021934
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.21093
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21714
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2154
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.242
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1571.51598
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.74622463
X-RAY DIFFRACTIONr_scbond_it2.66931057
X-RAY DIFFRACTIONr_scangle_it3.8344.5944
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.003→2.055 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 119 -
Rwork0.217 2229 -
all-2348 -
obs--100 %
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)
12.29891.228-0.38563.0186-1.58463.46-0.02950.0847-0.03430.193-0.0528-0.3378-0.07890.67820.0822-0.1944-0.0190.01890.11840.04760.074530.04514.8643
21.94360.60850.27981.5738-0.38562.4392-0.10690.3175-0.0267-0.1724-0.0308-0.06320.06210.30720.1376-0.1633-0.00070.0111-0.06790.0195-0.005417.94510.392-1.031
32.35160.41410.79892.5492-0.28363.32960.0079-0.00310.28460.1939-0.0691-0.0008-0.58060.00590.06120.0484-0.0103-0.0467-0.2451-0.02750.013214.9930.09716.605
41.89270.68110.36532.048-0.27862.7423-0.0186-0.20.09510.3315-0.12090.0361-0.3684-0.04820.1395-0.0472-0.0045-0.0189-0.1556-0.00660.002210.7417.61221.052
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 69
2X-RAY DIFFRACTION2A71 - 175
3X-RAY DIFFRACTION3B15 - 60
4X-RAY DIFFRACTION4B71 - 177

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