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- PDB-2uyc: HhaI DNA methyltransferase R163N mutant complex with 13mer GCGC-G... -

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Basic information

Entry
Database: PDB / ID: 2uyc
TitleHhaI DNA methyltransferase R163N mutant complex with 13mer GCGC-GMGC oligonucleotide and SAH
Components
  • 5'-D(*GP*TP*CP*AP*GP*CP*GP*CP*AP*TP *CP*C)-3'
  • 5'-D(*TP*GP*GP*AP*TP*GP*5CMP*GP*CP*TP *GP*AP*C)-3'
  • MODIFICATION METHYLASE HHAI
KeywordsTRANSFERASE / S-ADENOSYL-L-METHIONINE / BASE FLIPPING / METHYLTRANSFERASE / RESTRICTION SYSTEM / 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
S-ADENOSYL-L-HOMOCYSTEINE / DNA / DNA (> 10) / Type II methyltransferase M.HhaI
Similarity search - Component
Biological speciesHAEMOPHILUS HAEMOLYTICUS (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDaujotyte, D. / Grazulis, S.
CitationJournal: To be Published
Title: HhaI DNA Methyltransferase R163N Mutant Complex with 13mer Gcgc-Gmgc Oligonucleotide and Sah
Authors: Daujotyte, D. / Grazulis, S.
History
DepositionApr 3, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen / pdbx_entity_src_syn / Item: _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.4Jul 24, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MODIFICATION METHYLASE HHAI
C: 5'-D(*TP*GP*GP*AP*TP*GP*5CMP*GP*CP*TP *GP*AP*C)-3'
D: 5'-D(*GP*TP*CP*AP*GP*CP*GP*CP*AP*TP *CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,06515
Polymers44,6443
Non-polymers1,42112
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7290 Å2
ΔGint-74.3 kcal/mol
Surface area16030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.990, 94.990, 312.903
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-2116-

HOH

DetailsREMARK: BASED ON PREVIOUS STRUCTURES OF HHAI METHYLTRANSFERASEAND BIOCHEMICAL EXPERIMENTS, THE TERNARY COMPLEX HHAIMETHYLTRANSFERASE-DNA-SAH IS MONOMERIC

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Components

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Protein , 1 types, 1 molecules A

#1: Protein MODIFICATION METHYLASE HHAI / CYTOSINE-SPECIFIC METHYLTRANSFERASE HHAI / MHHAI / HHAI DNA METHYLTRANSFERASE


Mass: 36999.117 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HAEMOPHILUS HAEMOLYTICUS (bacteria) / Plasmid: PHH5.3 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2267
References: UniProt: P05102, DNA (cytosine-5-)-methyltransferase

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DNA chain , 2 types, 2 molecules CD

#2: DNA chain 5'-D(*TP*GP*GP*AP*TP*GP*5CMP*GP*CP*TP *GP*AP*C)-3'


Mass: 4021.636 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain 5'-D(*GP*TP*CP*AP*GP*CP*GP*CP*AP*TP *CP*C)-3'


Mass: 3623.368 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 246 molecules

#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, ARG 163 TO ASN
Sequence detailsMUTATION R163N

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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: 2.95 Å3/Da / Density % sol: 58 % / Description: NONE
Crystal growpH: 5.6
Details: 50 MM NA CITRATE PH 5.6, 1.8 M AMMONIUM SULFATE, 5% GLUCOSE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8063
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 14, 2006 / Details: MIRRORS
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8063 Å / Relative weight: 1
ReflectionResolution: 2→43.15 Å / Num. obs: 36938 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.6
Reflection shellResolution: 2→2.11 Å / Redundancy: 5 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 4.6 / % possible all: 99.7

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3MHT

3mht


Resolution: 2→36.41 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 32293104.37 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: RESOLUTION-DEPENDENT WEIGHTING SCHEME USED OTHER REFINEMENT REMARKS BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.227 3722 10.1 %RANDOM
Rwork0.2 ---
obs0.2 36937 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.5062 Å2 / ksol: 0.397357 e/Å3
Displacement parametersBiso mean: 19.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.92 Å20 Å2
2--0.02 Å20 Å2
3----0.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2→36.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2603 511 86 234 3434
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.04
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.691.5
X-RAY DIFFRACTIONc_mcangle_it1.142
X-RAY DIFFRACTIONc_scbond_it0.942
X-RAY DIFFRACTIONc_scangle_it1.572.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.266 555 9.5 %
Rwork0.235 5299 -
obs--95.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
X-RAY DIFFRACTION42AP.PAR2AP.TOP
X-RAY DIFFRACTION55MC.PAR5MC.TOP
X-RAY DIFFRACTION6SAH.PARSAH.TOP
X-RAY DIFFRACTION7SO4.PARSO4.TOP
X-RAY DIFFRACTION8GOL.PARGOL.TOP

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