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- PDB-2i9k: Engineered Extrahelical Base Destabilization Enhances Sequence Di... -

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Basic information

Entry
Database: PDB / ID: 2i9k
TitleEngineered Extrahelical Base Destabilization Enhances Sequence Discrimination of DNA Methyltransferase M.HhaI
Components
  • 5'-D(*T*GP*AP*TP*AP*GP*CP*GP*CP*TP*AP*TP*C)-3'
  • Modification methylase HhaI
KeywordsTRANSFERASE/DNA / Phe124Ala mutation in M.HhaI / 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 / Resolution: 2.65 Å
AuthorsYoungblood, B. / Shieh, F.K. / De Los Rios, S. / Perona, J.J. / Reich, N.O.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Engineered Extrahelical Base Destabilization Enhances Sequence Discrimination of DNA Methyltransferase M.HhaI
Authors: Youngblood, B. / Shieh, F.K. / De Los Rios, S. / Perona, J.J. / Reich, N.O.
History
DepositionSep 5, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: 5'-D(*T*GP*AP*TP*AP*GP*CP*GP*CP*TP*AP*TP*C)-3'
D: 5'-D(*T*GP*AP*TP*AP*GP*CP*GP*CP*TP*AP*TP*C)-3'
A: Modification methylase HhaI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2844
Polymers44,8993
Non-polymers3841
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-15 kcal/mol
Surface area15890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.510, 97.510, 319.700
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(*T*GP*AP*TP*AP*GP*CP*GP*CP*TP*AP*TP*C)-3'


Mass: 3966.597 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein Modification methylase HhaI / Cytosine-specific methyltransferase HhaI / M.HhaI


Mass: 36966.109 Da / Num. of mol.: 1 / Mutation: F124A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus haemolyticus (bacteria) / Gene: hhaIM / Plasmid: pHSHW-5 / Production host: Escherichia coli (E. coli) / Strain (production host): ER1727 / References: UniProt: P05102, EC: 2.1.1.73
#3: 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

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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: 3.25 Å3/Da / Density % sol: 62.15 %
Crystal growTemperature: 290 K / pH: 6
Details: 20% Ammonium Sulfate, 100mM Sodium Citrate buffer, pH 6.0, hanging drop, temperature 290K
Components of the solutions
IDNameCrystal-IDSol-ID
1Ammonium Sulfate11
2Sodium Citrate buffer11
3HOH11
4Ammonium Sulfate12
5Sodium Citrate buffer12
6HOH12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.541 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jul 15, 2004
RadiationMonochromator: Ni MIRROR + Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 2.65→8.38 Å / Num. obs: 17397 / % possible obs: 99.6 % / Observed criterion σ(F): 1.9 / Observed criterion σ(I): 1.9 / Rmerge(I) obs: 0.084 / Rsym value: 0.061 / Net I/σ(I): 7.1
Reflection shellResolution: 2.65→2.79 Å / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 1.9 / Num. unique all: 2096 / Rsym value: 0.287 / % possible all: 97.1

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementResolution: 2.65→2.79 Å / σ(F): 1.9 / σ(I): 1.9
RfactorNum. reflection% reflection
Rfree0.262 2096 -
Rwork0.238 --
all0.39 --
obs0.287 17397 99.6 %
Refinement stepCycle: LAST / Resolution: 2.65→2.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2587 506 26 0 3119
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_bond_d0.0075

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