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- PDB-9mht: CYTOSINE-SPECIFIC METHYLTRANSFERASE HHAI/DNA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 9mht
TitleCYTOSINE-SPECIFIC METHYLTRANSFERASE HHAI/DNA COMPLEX
Components
  • 5'-D(P*CP*CP*AP*TP*GP*CP*GP*CP*TP*GP*AP*C)-3'
  • 5'-D(P*GP*TP*CP*AP*GP*(3DR)P*GP*CP*AP*TP*GP*G)-3'
  • CYTOSINE-SPECIFIC METHYLTRANSFERASE HHAI
KeywordsTRANSFERASE/DNA / TRANSFERASE / METHYLTRANSFERASE / RESTRICTION SYSTEM / COMPLEX (METHYLTRANSFERASE- DNA) / 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 / OTHER / Resolution: 2.39 Å
AuthorsO'Gara, M. / Horton, J.R. / Roberts, R.J. / Cheng, X.
CitationJournal: Nat.Struct.Biol. / Year: 1998
Title: Structures of HhaI methyltransferase complexed with substrates containing mismatches at the target base.
Authors: O'Gara, M. / Horton, J.R. / Roberts, R.J. / Cheng, X.
History
DepositionAug 7, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Dec 1, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: 5'-D(P*CP*CP*AP*TP*GP*CP*GP*CP*TP*GP*AP*C)-3'
D: 5'-D(P*GP*TP*CP*AP*GP*(3DR)P*GP*CP*AP*TP*GP*G)-3'
A: CYTOSINE-SPECIFIC METHYLTRANSFERASE HHAI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6444
Polymers44,2603
Non-polymers3841
Water4,360242
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 settinghexagonal
Space group name H-MH32

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Components

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


Mass: 3623.368 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(P*GP*TP*CP*AP*GP*(3DR)P*GP*CP*AP*TP*GP*G)-3'


Mass: 3594.330 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein CYTOSINE-SPECIFIC METHYLTRANSFERASE HHAI / EC 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) / Production host: Escherichia coli (E. coli) / References: UniProt: P05102, EC: 2.1.1.73
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 3.53 Å3/Da / Density % sol: 65.11 %
Crystal growpH: 5.6
Details: 10% (W/V) POLYETHYLENE GLYCOL 8000 50 MM CA-ACETATE 50 MM SODIUM CACODYLATE PH 5.6
Components of the solutions
IDNameCrystal-IDSol-ID
1SODIUM CACODYLATE11
2CALCIUM ACETATE11
3PEG 800011
4PEG 800012
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 %(w/v)PEG80001drop
250 mMCa-acetate1drop
350 mMsodium cacodylate1drop
450 mMsodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.15
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.15 Å / Relative weight: 1
ReflectionResolution: 2.39→23 Å / Num. obs: 22634 / % possible obs: 91.6 % / Redundancy: 2.73 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 16.8
Reflection
*PLUS
Observed criterion σ(I): 0 / Num. measured all: 61880

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER
Starting model: PDB ENTRY 5MHT

5mht


Resolution: 2.39→6 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.186 --
obs0.186 20979 90 %
all-20979 -
Refinement stepCycle: LAST / Resolution: 2.39→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2606 484 26 242 3358
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.5
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: 2.39→2.49 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rwork0.24 1544 -
obs--53 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.5

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