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- PDB-5mht: TERNARY STRUCTURE OF HHAI METHYLTRANSFERASE WITH HEMIMETHYLATED D... -

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Basic information

Entry
Database: PDB / ID: 5mht
TitleTERNARY STRUCTURE OF HHAI METHYLTRANSFERASE WITH HEMIMETHYLATED DNA AND ADOHCY
Components
  • DNA (5'-D(*CP*CP*AP*TP*GP*(5CM)P*GP*CP*TP*GP*AP*C)-3')
  • DNA (5'-D(*GP*TP*CP*AP*GP*CP*GP*CP*AP*TP*GP*G)-3')
  • PROTEIN (HHAI METHYLTRANSFERASE)
KeywordsTRANSFERASE/DNA / TRANSFERASE / METHYLTRANSFERASE / RESTRICTION SYSTEM / COMPLEX (METHYLTRANSFERASE-DNA) / TRANSFERASE-DNA complex
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsCheng, X.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: A structural basis for the preferential binding of hemimethylated DNA by HhaI DNA methyltransferase.
Authors: O'Gara, M. / Roberts, R.J. / Cheng, X.
#1: Journal: J.Mol.Biol. / Year: 1996
Title: Enzymatic C5-Cytosine Methylation of DNA: Mechanistic Implications of New Crystal Structures for HhaI Methyltransferase-DNA-Adohcy Complexes
Authors: O'Gara, M. / Klimasauskas, S. / Roberts, R.J. / Cheng, X.
#2: Journal: Cell(Cambridge,Mass.) / Year: 1994
Title: HhaI Methyltransferase Flips its Target Base Out of the DNA Helix
Authors: Klimasauskas, S. / Kumar, S. / Roberts, R.J. / Cheng, X.
#3: Journal: Cell(Cambridge,Mass.) / Year: 1993
Title: Crystal Structure of the HhaI DNA Methyltransferase Complexed with S-Adenosyl- L-Methionine
Authors: Cheng, X. / Kumar, S. / Posfai, J. / Pflugrath, J.W. / Roberts, R.J.
History
DepositionOct 22, 1996Deposition site: BNL / Processing site: NDB
Revision 1.0Jul 23, 1997Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA (5'-D(*CP*CP*AP*TP*GP*(5CM)P*GP*CP*TP*GP*AP*C)-3')
D: DNA (5'-D(*GP*TP*CP*AP*GP*CP*GP*CP*AP*TP*GP*G)-3')
A: PROTEIN (HHAI METHYLTRANSFERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7674
Polymers44,3833
Non-polymers3841
Water2,018112
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.860, 99.860, 325.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: DNA chain DNA (5'-D(*CP*CP*AP*TP*GP*(5CM)P*GP*CP*TP*GP*AP*C)-3')


Mass: 3637.395 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*GP*TP*CP*AP*GP*CP*GP*CP*AP*TP*GP*G)-3')


Mass: 3703.416 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein PROTEIN (HHAI METHYLTRANSFERASE) / E.C.2.1.1.7 / MODIFICATION METHYLASE HHAI / CYTOSINE-SPECIFIC METHYLTRANSFERASE HHAI / M.HHAI


Mass: 37042.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haemophilus haemolyticus (bacteria) / References: UniProt: P05102, EC: 2.1.1.7
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 3.52 Å3/Da / Density % sol: 65.01 %
Crystal growpH: 6.5
Details: 10% PEG 8000, 50 MM CA-ACETATE, 50 MM SODIUM CACODYLATE PH 6.5
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 %(w/v)PEG800011
250 mMCa-acetate11or Mg-acetate
350 mMsodium cacodylate11

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 16761 / % possible obs: 95.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0.5 / Redundancy: 4.6 % / Rmerge(I) obs: 0.077
Reflection
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 30 Å / Observed criterion σ(I): 1 / Redundancy: 4.6 %

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.7→20 Å / σ(F): 1
Details: WATER MOLECULE 345 IS SURROUNDED BY THREE POSITIVELY CHANGED RESIDUES: ARG 245, LYS 193, AND SYMMETRY-RELATED LYS 290. HOWEVER, THE DENSITY IS NOT GOOD ENOUGH TO IDENTIFY WHAT IT MIGHT BE. ...Details: WATER MOLECULE 345 IS SURROUNDED BY THREE POSITIVELY CHANGED RESIDUES: ARG 245, LYS 193, AND SYMMETRY-RELATED LYS 290. HOWEVER, THE DENSITY IS NOT GOOD ENOUGH TO IDENTIFY WHAT IT MIGHT BE. WATER MOLECULE 392 IS SITUATED IN BETWEEN TWO DNA PHOSPHATE GROUPS OF A 430 D AND T 431 D. CA-ACETATE WAS USED AS BUFFER. HOWEVER, THE DENSITY IS NOT GOOD ENOUGH TO DETERMINE WHETHER IT IS A CA(2+) FOR SURE.
RfactorNum. reflection% reflection
Rwork0.188 --
obs0.188 16743 95.1 %
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2734 493 27 112 3366
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d1.7
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d29.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
LS refinement shellResolution: 2.7→2.82 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rwork0.271 1733 -
obs--80.6 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 20 Å / σ(F): 1
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg29.8
X-RAY DIFFRACTIONx_improper_angle_deg1.5
LS refinement shell
*PLUS
Rfactor obs: 0.271

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