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- PDB-1skm: HhaI methyltransferase in complex with DNA containing an abasic s... -

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Basic information

Entry
Database: PDB / ID: 1skm
TitleHhaI methyltransferase in complex with DNA containing an abasic south carbocyclic sugar at its target site
Components
  • 5'-D(*T*GP*TP*CP*AP*GP*(HCX)P*GP*CP*AP*TP*GP*G)-3'
  • 5'-D(*TP*CP*CP*AP*TP*GP*CP*GP*CP*TP*GP*AP*C)-3'
  • Modification methylase HhaI
KeywordsTRANSFERASE/DNA / PROTEIN-DNA COMPLEX Containing Constrained Abasic Unnatural base / 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 / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHorton, J.R. / Ratner, G. / Banavali, N. / Huang, N. / Marquez, V.E. / MacKerell, A.D. / Cheng, X.
CitationJournal: Nucleic Acids Res. / Year: 2004
Title: Caught in the act: visualization of an intermediate in the DNA base-flipping pathway induced by HhaI methyltransferase
Authors: Horton, J.R. / Ratner, G. / Banavali, N.K. / Huang, N. / Choi, Y. / Maier, M.A. / Marquez, V.E. / MacKerell, A.D. / Cheng, X.
History
DepositionMar 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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: 5'-D(*TP*CP*CP*AP*TP*GP*CP*GP*CP*TP*GP*AP*C)-3'
D: 5'-D(*T*GP*TP*CP*AP*GP*(HCX)P*GP*CP*AP*TP*GP*G)-3'
A: Modification methylase HhaI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2474
Polymers44,8623
Non-polymers3841
Water4,630257
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.681, 95.681, 315.683
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 5'-D(*TP*CP*CP*AP*TP*GP*CP*GP*CP*TP*GP*AP*C)-3'


Mass: 3927.561 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*T*GP*TP*CP*AP*GP*(HCX)P*GP*CP*AP*TP*GP*G)-3'


Mass: 3892.561 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein Modification methylase HhaI / Cytosine-specific methyltransferase HhaI / M.HhaI


Mass: 37042.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus haemolyticus (bacteria) / Gene: HHAIM / Production host: Escherichia coli (E. coli)
References: UniProt: P05102, DNA (cytosine-5-)-methyltransferase
#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.: 257 / 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: 3.08 Å3/Da / Density % sol: 60.04 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 6000, sodium cacodylate, magnesium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 600011
2sodium cacodylate11
3magnesium acetate11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 20, 2001
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.2→24.53 Å / Num. all: 24477 / Num. obs: 23477 / % possible obs: 81.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 13.5 Å2 / Rsym value: 0.067 / Net I/σ(I): 18.4
Reflection shellResolution: 2.2→2.25 Å / Rmerge(I) obs: 0.179 / Num. unique all: 689 / % possible all: 36.9

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Processing

Software
NameClassification
CAD4data collection
SCALEPACKdata scaling
GLRFphasing
CNSrefinement
CAD4data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→24.53 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.221 1134 -random
Rwork0.183 ---
obs0.183 23477 81.9 %-
all-23477 --
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.74 Å21.85 Å2-2.58 Å2
2--2.3 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-25 Å
Luzzati sigma a0.26 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.2→24.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2591 499 26 257 3373
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONBond Lengths0.007
X-RAY DIFFRACTIONBond Angles1.2
X-RAY DIFFRACTIONDIHEDRAL ANGLES22.4
X-RAY DIFFRACTIONIMPROPER ANGLES1.6
LS refinement shellResolution: 2.2→2.25 Å / Rfactor Rfree error: 0.065
RfactorNum. reflection% reflection
Rfree0.303 22 -
Rwork0.261 --
obs--34 %

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