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- PDB-1g60: Crystal Structure of Methyltransferase MboIIa (Moraxella bovis) -

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Basic information

Entry
Database: PDB / ID: 1g60
TitleCrystal Structure of Methyltransferase MboIIa (Moraxella bovis)
ComponentsAdenine-specific Methyltransferase MboIIA
KeywordsTRANSFERASE / STRUCTURAL GENOMICS / MORAXELLA BOVIS / DNA METHYLATION / S-ADENOSYLMETHIONINE / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


N-methyltransferase activity / site-specific DNA-methyltransferase (adenine-specific) / site-specific DNA-methyltransferase (adenine-specific) activity / DNA restriction-modification system / methylation / DNA binding / cytoplasm
Similarity search - Function
Restriction/modification DNA-methyltransferase / DNA methylase N-4/N-6 / DNA methylase / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / Type II methyltransferase M1.MboII
Similarity search - Component
Biological speciesMoraxella bovis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.74 Å
AuthorsOsipiuk, J. / Walsh, M.A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
Citation
Journal: Nucleic Acids Res. / Year: 2003
Title: Crystal structure of MboIIA methyltransferase.
Authors: Osipiuk, J. / Walsh, M.A. / Joachimiak, A.
#1: Journal: Nucleic Acids Res. / Year: 1991
Title: Cloning and Characterization of the MboII Restriction-modification System
Authors: Bocklage, H. / Heeger, K. / Muller-Hill, B.
History
DepositionNov 2, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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
Remark 999SEQUENCE DNA SEQUENCING OF THE CLONES SHOWED THERE IS A ALANINE CODON FOR RESIDUE 51 AND A ARGININE ...SEQUENCE DNA SEQUENCING OF THE CLONES SHOWED THERE IS A ALANINE CODON FOR RESIDUE 51 AND A ARGININE CODON FOR RESIDUE 111.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adenine-specific Methyltransferase MboIIA
B: Adenine-specific Methyltransferase MboIIA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2286
Polymers60,3852
Non-polymers8434
Water6,503361
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-36 kcal/mol
Surface area22890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.818, 98.699, 50.894
Angle α, β, γ (deg.)90.00, 101.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Adenine-specific Methyltransferase MboIIA / Modification methylase MboIIA


Mass: 30192.391 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moraxella bovis (bacteria) / Plasmid: PET24A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS
References: UniProt: P23192, site-specific DNA-methyltransferase (adenine-specific)
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / 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: 2.47 Å3/Da / Density % sol: 50.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 4% PEG monomethyl ether 5000, 50 mM potassium chloride, 50 mM sodium chloride, 1 mM DTT, 50 mM bicine, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Crystal grow
*PLUS
Temperature: 277 K / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.5 mMprotein1drop
25 mMTris-HCl1droppH7.5
375 mM1dropKCl
41 mMdithiothreitol1drop
5100 mMBicine1reservoirpH8.4
64 %PEG5000 MME1reservoir
750 mM1reservoirKCl
850 mM1reservoirNaCl
91 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.00599 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Aug 29, 1999
RadiationMonochromator: SI 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00599 Å / Relative weight: 1
ReflectionResolution: 1.74→28.79 Å / Num. obs: 60668 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.72 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 12.1
Reflection shellResolution: 1.74→1.77 Å / Redundancy: 3.63 % / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 3.4 / Num. unique all: 2974 / % possible all: 99.4
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 60068
Reflection shell
*PLUS
% possible obs: 99.4 %

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
REFMACrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.74→29.75 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.221 2417 -RANDOM
Rwork0.198 ---
all0.199 ---
obs0.199 59974 99.6 %-
Displacement parametersBiso mean: 27.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å20.7 Å2-1.66 Å2
2--0 Å2-0.19 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.74→29.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3888 0 56 361 4305
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.0270.04
X-RAY DIFFRACTIONp_planar_d0.0310.05
LS refinement shellResolution: 1.74→1.826 Å
RfactorNum. reflection
Rfree0.289 306
Rwork0.224 -
obs-8029
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor obs: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS

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