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- PDB-3lby: Crystal structure of SMU.1697c, a putative methyltransferase from... -

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Basic information

Entry
Database: PDB / ID: 3lby
TitleCrystal structure of SMU.1697c, a putative methyltransferase from streptococcus mutans in complex with SAH
ComponentsPutative uncharacterized protein SMU.1697c
KeywordsTRANSFERASE / methyltransferase / streptococcus mutans / SAH
Function / homologyPutative rRNA methylase / Putative rRNA methylase / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / S-ADENOSYL-L-HOMOCYSTEINE / rRNA methylase
Function and homology information
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsWang, K.-T. / Nan, J. / Su, X.-D.
CitationJournal: To be published
Title: Crystal structure of SMU.1697c, a putative methyltransferase from streptococcus mutans in complex with SAH
Authors: Wang, K.-T. / Nan, J. / Su, X.-D.
History
DepositionJan 8, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 30, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Putative uncharacterized protein SMU.1697c
B: Putative uncharacterized protein SMU.1697c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3903
Polymers41,0062
Non-polymers3841
Water4,522251
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-16 kcal/mol
Surface area15330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.210, 92.210, 107.010
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-185-

HOH

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Components

#1: Protein Putative uncharacterized protein SMU.1697c


Mass: 20502.779 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Gene: SMU_1697c / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DSS3
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 3.2 Å3/Da / Density % sol: 61.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M Bis-tris pH5.5, 1.0M Na Formate, 15% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.97 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 20, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.98→30 Å / Num. obs: 35822 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Biso Wilson estimate: 34.15 Å2
Reflection shellResolution: 1.98→2.09 Å / % possible all: 82

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Processing

Software
NameVersionClassification
SOLVEphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2→26.601 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.845 / SU ML: 0.31 / σ(F): 1.34 / Phase error: 22.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2441 2012 5.62 %
Rwork0.2104 33809 -
obs0.2123 35821 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 91.076 Å2 / ksol: 0.369 e/Å3
Displacement parametersBiso max: 162.84 Å2 / Biso mean: 48.808 Å2 / Biso min: 19.46 Å2
Baniso -1Baniso -2Baniso -3
1--0.255 Å2-0 Å20 Å2
2---0.255 Å2-0 Å2
3---0.51 Å2
Refinement stepCycle: LAST / Resolution: 2→26.601 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2496 0 26 251 2773
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062575
X-RAY DIFFRACTIONf_angle_d1.0273496
X-RAY DIFFRACTIONf_dihedral_angle_d17.02928
X-RAY DIFFRACTIONf_chiral_restr0.071430
X-RAY DIFFRACTIONf_plane_restr0.004439
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.28611470.24912426X-RAY DIFFRACTION100
2.05-2.10540.26431400.24222370X-RAY DIFFRACTION100
2.1054-2.16740.28561400.22562386X-RAY DIFFRACTION100
2.1674-2.23730.25661480.2092404X-RAY DIFFRACTION100
2.2373-2.31720.22981460.19132422X-RAY DIFFRACTION100
2.3172-2.40990.24651440.19652371X-RAY DIFFRACTION100
2.4099-2.51950.2651410.20222420X-RAY DIFFRACTION100
2.5195-2.65220.26551460.21112408X-RAY DIFFRACTION100
2.6522-2.81820.27041430.22282423X-RAY DIFFRACTION100
2.8182-3.03560.25221400.21032428X-RAY DIFFRACTION100
3.0356-3.34050.23861440.20252441X-RAY DIFFRACTION100
3.3405-3.82270.23681460.18672459X-RAY DIFFRACTION100
3.8227-4.81150.17261480.17252447X-RAY DIFFRACTION99
4.8115-26.60330.26921390.24262404X-RAY DIFFRACTION93
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)
12.1161-0.47970.46881.66760.4993.03090.1422-0.10660.0906-0.2221-0.2140.0089-0.1182-0.07680.08590.07430.05680.0430.2396-0.03140.13915.121238.67062.2443
21.4461-1.62130.18732.04640.36572.2996-0.2932-0.78670.28590.38090.2047-0.0456-0.01650.13640.01240.11890.01720.00360.737-0.1210.211716.946142.66931.8269
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA1 - 181
2X-RAY DIFFRACTION2chain BB1 - 181

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