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- PDB-2b78: A putative sam-dependent methyltransferase from Streptococcus mutans -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 2b78
TitleA putative sam-dependent methyltransferase from Streptococcus mutans
Componentshypothetical protein SMU.776Hypothesis
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / structure genomics / METHYLTRANSFERASE / caries
Function / homology
Function and homology information


methyltransferase activity / methylation / RNA binding
Similarity search - Function
RlmI, PUA-like domain / PUA-like domain / RNA methyltransferase domain (HRMD) like / S-adenosylmethionine-dependent methyltransferase / S-adenosylmethionine-dependent methyltransferase / PUA domain / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / Transcription Regulator spoIIAA / PUA domain superfamily / PUA-like superfamily ...RlmI, PUA-like domain / PUA-like domain / RNA methyltransferase domain (HRMD) like / S-adenosylmethionine-dependent methyltransferase / S-adenosylmethionine-dependent methyltransferase / PUA domain / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / Transcription Regulator spoIIAA / PUA domain superfamily / PUA-like superfamily / Vaccinia Virus protein VP39 / Roll / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 2 Å
AuthorsNan, J. / Wang, K.T. / Su, X.D.
CitationJournal: To be Published
Title: A putative sam-dependent methyltransferase from Streptococcus mutans
Authors: Nan, J. / Wang, K.T. / Su, X.D.
History
DepositionOct 3, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 31, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 18, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein SMU.776


Theoretical massNumber of molelcules
Total (without water)43,7351
Polymers43,7351
Non-polymers00
Water3,963220
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)168.472, 50.659, 53.963
Angle α, β, γ (deg.)90.00, 104.22, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein hypothetical protein SMU.776 / Hypothesis


Mass: 43734.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8DUW5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.5251.3
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2891vapor diffusion, hanging drop6.5PEG8000, Sodium Cacodylate,Magnesium Acetates, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
2892vapor diffusion, hanging drop6.5PEG8000, Sodium Cacodylate,Magnesium Acetates, ethyl mercury thiosalicylate , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceTypeIDWavelength (Å)
ROTATING ANODEENRAF-NONIUS FR59111.5418
ROTATING ANODEENRAF-NONIUS FR59121.5418
Detector
TypeIDDetectorDateDetails
BRUKER SMART 60001CCDMar 17, 2005MONTEL
BRUKER SMART 60002CCDMar 22, 2005MONTEL
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MONTELSINGLE WAVELENGTHMx-ray1
2MONTELSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 58372 / Num. obs: 52534 / % possible obs: 94.49 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.54 % / Rsym value: 0.0503 / Net I/σ(I): 11
Reflection shellResolution: 1.8→1.91 Å / Mean I/σ(I) obs: 2.77 / Rsym value: 0.1509 / % possible all: 74.1

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT1.7data extraction
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
SOLVEphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2→50 Å / Isotropic thermal model: anisotropic / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 5086 8.7 %RANDOM
Rwork0.241 ---
all-41078 --
obs-38816 90 %-
Solvent computationBsol: 37.563 Å2
Displacement parametersBiso mean: 20.246 Å2
Baniso -1Baniso -2Baniso -3
1-1.084 Å20 Å21.445 Å2
2---3.184 Å20 Å2
3---2.1 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3014 0 0 220 3234
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water.param

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