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- PDB-5lod: Crystal structure of HhaI DNA methyltransferase in APO form -

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Basic information

Entry
Database: PDB / ID: 5lod
TitleCrystal structure of HhaI DNA methyltransferase in APO form
ComponentsModification methylase HhaI
KeywordsTRANSFERASE / M.HhaI / C5-METHYLCYTOSINE / APO FORM / DNA methyltransferase
Function / homology
Function and homology information


DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / DNA restriction-modification system / DNA binding
Similarity search - Function
DNA Methylase, subunit A, domain 2 / DNA Methylase; Chain A, domain 2 / DNA methylase, C-5 cytosine-specific, conserved site / C-5 cytosine-specific DNA methylases C-terminal signature. / DNA methylase, C-5 cytosine-specific, active site / C-5 cytosine-specific DNA methylases active site. / C-5 cytosine-specific DNA methylase (Dnmt) domain profile. / C-5 cytosine methyltransferase / C-5 cytosine-specific DNA methylase / Vaccinia Virus protein VP39 ...DNA Methylase, subunit A, domain 2 / DNA Methylase; Chain A, domain 2 / DNA methylase, C-5 cytosine-specific, conserved site / C-5 cytosine-specific DNA methylases C-terminal signature. / DNA methylase, C-5 cytosine-specific, active site / C-5 cytosine-specific DNA methylases active site. / C-5 cytosine-specific DNA methylase (Dnmt) domain profile. / C-5 cytosine methyltransferase / C-5 cytosine-specific DNA methylase / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Type II methyltransferase M.HhaI
Similarity search - Component
Biological speciesHaemophilus parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRondelet, G. / Wouters, J.
Funding support Belgium, 1items
OrganizationGrant numberCountry
F.R.S._FNRS_Televie7.4.532.15.F. Belgium
CitationJournal: Future Med Chem / Year: 2017
Title: Inhibition studies of DNA methyltransferases by maleimide derivatives of RG108 as non-nucleoside inhibitors.
Authors: Rondelet, G. / Fleury, L. / Faux, C. / Masson, V. / Dubois, J. / Arimondo, P.B. / Willems, L. / Wouters, J.
History
DepositionAug 9, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 10, 2024Group: 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
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
B: Modification methylase HhaI
A: Modification methylase HhaI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5657
Polymers74,0842
Non-polymers4805
Water4,432246
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-75 kcal/mol
Surface area26610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.000, 70.000, 87.800
Angle α, β, γ (deg.)90.000, 101.300, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Modification methylase HhaI / M.HhaI / Cytosine-specific methyltransferase HhaI


Mass: 37042.207 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus parahaemolyticus (bacteria)
Gene: hhaIM / Production host: Escherichia coli (E. coli)
References: UniProt: P05102, DNA (cytosine-5-)-methyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.16 Å3/Da / Density % sol: 42.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: AMMONIUM SULFATE 50 mM, CITRATE 100mM, 32% (w/v) PEG-4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Type: OTHER / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.9→41.73 Å / Num. obs: 49539 / % possible obs: 99.61 % / Redundancy: 3.68 % / CC1/2: 0.98 / Rmerge(I) obs: 0.058 / Net I/σ(I): 12.42
Reflection shellResolution: 1.9→1.968 Å / Redundancy: 3.57 % / Rmerge(I) obs: 0.429 / Mean I/σ(I) obs: 2.77 / CC1/2: 0.907 / % possible all: 99.74

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HMY

2hmy


Resolution: 1.9→41.728 Å / FOM work R set: 0.8508 / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2194 2476 5 %
Rwork0.1784 47041 -
obs0.1804 49517 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.53 Å2 / Biso mean: 34.54 Å2 / Biso min: 16.88 Å2
Refinement stepCycle: final / Resolution: 1.9→41.728 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5122 0 25 246 5393
Biso mean--41.65 39.54 -
Num. residues----642
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075250
X-RAY DIFFRACTIONf_angle_d1.0777084
X-RAY DIFFRACTIONf_chiral_restr0.074758
X-RAY DIFFRACTIONf_plane_restr0.005924
X-RAY DIFFRACTIONf_dihedral_angle_d13.921956
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.93660.26921320.218925702702100
1.9366-1.97610.27261440.216226072751100
1.9761-2.01910.25081370.210325782715100
2.0191-2.0660.27111320.208626222754100
2.066-2.11770.26571430.19626492792100
2.1177-2.17490.26231350.196525652700100
2.1749-2.23890.21211330.190526222755100
2.2389-2.31120.24911430.177826312774100
2.3112-2.39380.23061360.185826042740100
2.3938-2.48960.20791350.187525982733100
2.4896-2.60290.24931390.193126052744100
2.6029-2.74010.24231370.183326402777100
2.7401-2.91180.20771340.179826122746100
2.9118-3.13650.23271400.178326242764100
3.1365-3.4520.21621400.177526072747100
3.452-3.95120.21991380.164726312769100
3.9512-4.97680.16021380.15632638277699
4.9768-41.73850.23311400.18082638277897

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