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- PDB-2c7o: HhaI DNA methyltransferase complex with 13mer oligonucleotide con... -

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Basic information

Entry
Database: PDB / ID: 2c7o
TitleHhaI DNA methyltransferase complex with 13mer oligonucleotide containing 2-aminopurine adjacent to the target base (PCGC:GMGC) and SAH
Components
  • 5'-D(*T*GP*GP*AP*TP*GP*(5CM)*GP*CP*TP*GP*AP *C)-3'
  • 5'-D(*T*GP*TP*CP*AP*(2PR)*CP*GP*CP*AP*TP*CP *C)-3'
  • MODIFICATION METHYLASE HHAI
KeywordsTRANSFERASE/DNA / TRANSFERASE-DNA COMPLEX / BASE FLIPPING / TRANSFERASE RESTRICTION SYSTEM
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: 1.9 Å
AuthorsDaujotyte, D. / Grazulis, S.
CitationJournal: Nucleic Acids Res. / Year: 2005
Title: Time-Resolved Fluorescence of 2-Aminopurine as a Probe of Base Flipping in M.HhaI-DNA Complexes.
Authors: Neely, R.K. / Daujotyte, D. / Grazulis, S. / Magennis, S.W. / Dryden, D.T.F. / Klimasauskas, S. / Jones, A.C.
History
DepositionNov 25, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2005Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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
A: MODIFICATION METHYLASE HHAI
C: 5'-D(*T*GP*GP*AP*TP*GP*(5CM)*GP*CP*TP*GP*AP *C)-3'
D: 5'-D(*T*GP*TP*CP*AP*(2PR)*CP*GP*CP*AP*TP*CP *C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7448
Polymers44,9753
Non-polymers7695
Water6,143341
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6200 Å2
ΔGint-45.5 kcal/mol
Surface area15890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.180, 95.180, 312.547
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-2128-

HOH

21A-2263-

HOH

31C-2001-

HOH

DetailsTHE OLIGOMERIC STATE OF HHAI METHYLTRANSFERASE IS MONOMERIC, BUT SINCE IN THIS ENTRY, THE PROTEIN IS IN COMPLEX WITH DNA, THE QUATERNARY STRUCTURE FOR THIS ENTRY IS MARKED AS TRIMERIC.

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 37042.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HAEMOPHILUS HAEMOLYTICUS (bacteria) / Plasmid: PHH553 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ER1727
References: UniProt: P05102, DNA (cytosine-5-)-methyltransferase

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DNA chain , 2 types, 2 molecules CD

#2: DNA chain 5'-D(*T*GP*GP*AP*TP*GP*(5CM)*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(*T*GP*TP*CP*AP*(2PR)*CP*GP*CP*AP*TP*CP *C)-3'


Mass: 3911.562 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Non-polymers , 3 types, 346 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.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 341 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsRECOGNIZES THE DOUBLE-STRANDED SEQUENCE GCGC, CAUSES SPECIFIC METHYLATION AND PROTECTS THE DNA FROM ...RECOGNIZES THE DOUBLE-STRANDED SEQUENCE GCGC, CAUSES SPECIFIC METHYLATION AND PROTECTS THE DNA FROM CLEAVAGE BY THE HHAI ENDONUCLEASE.

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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: 2.74 Å3/Da / Density % sol: 54.79 %
Crystal growpH: 5.6
Details: 50 MM NA CITRATE PH 5.6, 1.6 M AMMONIUM SULFATE, 5 % GLUCOSE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.812
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 18, 2004 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.812 Å / Relative weight: 1
ReflectionResolution: 1.9→23.2 Å / Num. obs: 43361 / % possible obs: 99.6 % / Observed criterion σ(I): 3.9 / Redundancy: 21.6 % / Biso Wilson estimate: 10.9 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 11.4
Reflection shellResolution: 1.9→2 Å / Redundancy: 20.8 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 3.9 / % possible all: 98.5

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Processing

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

3mht


Resolution: 1.9→23.08 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 34200167.59 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: RESOLUTION-DEPENDENT WEIGHTING SCHEME USED. BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.215 4391 10.1 %RANDOM
Rwork0.194 ---
obs0.194 43361 99.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.1244 Å2 / ksol: 0.385184 e/Å3
Displacement parametersBiso mean: 18.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.11 Å20.91 Å20 Å2
2--1.11 Å20 Å2
3----2.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.9→23.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2595 509 46 341 3491
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.08
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.451.5
X-RAY DIFFRACTIONc_mcangle_it0.782
X-RAY DIFFRACTIONc_scbond_it0.572
X-RAY DIFFRACTIONc_scangle_it0.992.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.227 726 10.3 %
Rwork0.217 6328 -
obs--98.4 %
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 DIFFRACTION6CIT.PARCIT.TOP
X-RAY DIFFRACTION7SAH.PARSAH.TOP
X-RAY DIFFRACTION8SO4.PARSO4.TOP

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