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- PDB-1mht: COVALENT TERNARY STRUCTURE OF HHAI METHYLTRANSFERASE, DNA AND S-A... -

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Basic information

Entry
Database: PDB / ID: 1mht
TitleCOVALENT TERNARY STRUCTURE OF HHAI METHYLTRANSFERASE, DNA AND S-ADENOSYL-L-HOMOCYSTEINE
Components
  • DNA (5'-D(*TP*GP*AP*TP*AP*GP*(C36)P*GP*CP*TP*AP*TP*C)-3')
  • DNA (5'-D(P*GP*AP*TP*AP*GP*(C36)P*GP*CP*TP*AP*TP*C)-3')
  • PROTEIN (HHAI METHYLTRANSFERASE)
KeywordsTRANSFERASE/DNA / PROTEIN-DNA COMPLEX / DOUBLE HELIX / OVERHANGING BASE / FLIPPED-OUT BASE / MODIFIED / TRANSFERASE-DNA COMPLEX
Function / homology
Function and homology information


DNA (cytosine-5-)-methyltransferase activity, acting on CpN substrates / DNA (cytosine-5-)-methyltransferase activity, acting on CpNpG substrates / DNA (cytosine-5-)-methyltransferase / DNA restriction-modification system / methylation / 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 ...: / 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: 2.6 Å
AuthorsCheng, X.
Citation
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.
#1: 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
DepositionDec 8, 1994Deposition site: BNL / Processing site: NDB
Revision 1.0Jun 3, 1995Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _chem_comp.mon_nstd_flag / _chem_comp.type ..._chem_comp.mon_nstd_flag / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
B: DNA (5'-D(P*GP*AP*TP*AP*GP*(C36)P*GP*CP*TP*AP*TP*C)-3')
C: DNA (5'-D(*TP*GP*AP*TP*AP*GP*(C36)P*GP*CP*TP*AP*TP*C)-3')
A: PROTEIN (HHAI METHYLTRANSFERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1564
Polymers44,7713
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)99.860, 99.860, 325.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Cell settingtrigonal
Space group name H-MH32

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Components

#1: DNA chain DNA (5'-D(P*GP*AP*TP*AP*GP*(C36)P*GP*CP*TP*AP*TP*C)-3')


Mass: 3712.436 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*TP*GP*AP*TP*AP*GP*(C36)P*GP*CP*TP*AP*TP*C)-3')


Mass: 4016.629 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein PROTEIN (HHAI METHYLTRANSFERASE) / E.C.2.1.1.73


Mass: 37042.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus haemolyticus (bacteria) / References: UniProt: P05102, EC: 2.1.1.73
#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
Has protein modificationY

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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: 3.51 Å3/Da / Density % sol: 65 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.25
Details: BIS-TRIS-PROPANE_HCL, NACL, EDTA, pH 7.25, VAPOR DIFFUSION, HANGING DROP, temperature 289.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2BIS-TRIS-PROPANE_HCL11
3NACL11
4EDTA11
5WATER12
6NH4 SULFATE12
7NA CITRATE12
Crystal grow
*PLUS
Temperature: 16 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15-10 mg/mlprotein1drop
210 mMTris-HCl1drop
350 mM1dropNaCl
40.5 mMNa2EDTA1drop
51.2-1.4 Mammonium sulfate1reservoir
650 mMsodium citrate1reservoir
71

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Type: NSLS / Wavelength: 1
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionHighest resolution: 2.8 Å / Num. obs: 17839 / Rmerge(I) obs: 0.0765
Reflection
*PLUS
Highest resolution: 2.8 Å

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Processing

Software
NameClassification
X-PLORrefinement
MADNESdata reduction
RefinementResolution: 2.6→10 Å /
RfactorNum. reflection
Rwork0.174 -
obs0.174 17839
Refinement stepCycle: LAST / Resolution: 2.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2606 495 46 0 3147
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.6

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