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- PDB-1boo: PVUII DNA METHYLTRANSFERASE (CYTOSINE-N4-SPECIFIC) -

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Basic information

Entry
Database: PDB / ID: 1boo
TitlePVUII DNA METHYLTRANSFERASE (CYTOSINE-N4-SPECIFIC)
ComponentsPROTEIN (N-4 CYTOSINE-SPECIFIC METHYLTRANSFERASE PVU II)
KeywordsTRANSFERASE / TYPE II DNA-(CYTOSINE N4) METHYLTRANSFERASE / AMINO METHYLATION / SELENOMETHIONINE / MULTIWAVELENGTH ANOMALOUS DIFFRACTION
Function / homology
Function and homology information


site-specific DNA-methyltransferase (cytosine-N4-specific) / site-specific DNA-methyltransferase (cytosine-N4-specific) activity / N-methyltransferase activity / DNA restriction-modification system / methylation / DNA binding
Similarity search - Function
DNA methylase, N-4 cytosine-specific, conserved site / N-4 cytosine-specific DNA methylases signature. / Restriction/modification DNA-methyltransferase / DNA methylase N-4/N-6 / DNA methylase / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Type II methyltransferase M.PvuII
Similarity search - Component
Biological speciesProteus vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsGong, W. / O'Gara, M. / Blumenthal, R.M. / Cheng, X.
Citation
Journal: Nucleic Acids Res. / Year: 1997
Title: Structure of pvu II DNA-(cytosine N4) methyltransferase, an example of domain permutation and protein fold assignment.
Authors: Gong, W. / O'Gara, M. / Blumenthal, R.M. / Cheng, X.
#1: Journal: Eur.J.Biochem. / Year: 1997
Title: Expression, Purification, Mass Spectrometry, Crystallization and Multiwavelength Anomalous Diffraction of Selenomethionyl PvuII DNA Methyltransferase (Cytosine-N4-Specific)
Authors: O'Gara, M. / Adams, G.M. / Gong, W. / Kobayashi, R. / Blumenthal, R.M. / Cheng, X.
History
DepositionJul 31, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 12, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (N-4 CYTOSINE-SPECIFIC METHYLTRANSFERASE PVU II)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3412
Polymers36,9561
Non-polymers3841
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.800, 112.400, 59.300
Angle α, β, γ (deg.)90.00, 109.20, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.6975, -0.6041, 0.3855), (-0.6016, -0.7859, -0.143), (0.3893, -0.1322, -0.9116)
Vector: 19.3519, 106.8, 81.2965)

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Components

#1: Protein PROTEIN (N-4 CYTOSINE-SPECIFIC METHYLTRANSFERASE PVU II) / EC 2.1.1.113


Mass: 36956.207 Da / Num. of mol.: 1
Fragment: STARTING FROM THE INTERNAL TRANSLATION INITIATOR AT MET14
Mutation: N TERMIANL DELETION (RESIDUES 1-13)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus vulgaris (bacteria) / Species (production host): Escherichia coli
Production host: Escherichia coli str. K-12 substr. DH10B (bacteria)
Strain (production host): DH10B
References: UniProt: P11409, site-specific DNA-methyltransferase (cytosine-N4-specific)
#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

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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

CrystalDensity Matthews: 4.15 Å3/Da / Density % sol: 38.2 %
Crystal growpH: 7.2
Details: 0.1 M HEPES PH 7.2, 0.2 M SODIUM ACETATE 20% POLYETHYLENE GLYCOL 400
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 MHEPES11
20.2 Msodium acetate11
320 %(w/v)PEG400011

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Data collection

DiffractionMean temperature: 289 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.98233,0.98211,0.92,1.072
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRRORS
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.982331
20.982111
30.921
41.0721
ReflectionResolution: 2.8→30 Å / Num. obs: 14886 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.68 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 11.5
Reflection shellResolution: 2.8→2.85 Å / Rmerge(I) obs: 0.226 / Mean I/σ(I) obs: 5.5 / % possible all: 97.5
Reflection
*PLUS
Num. measured all: 54787
Reflection shell
*PLUS
% possible obs: 97.5 %

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.8→30 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.283 -8 %RANDOM
Rwork0.193 ---
obs0.193 14886 99.7 %-
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2219 0 26 0 2245
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.2
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.2

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