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- PDB-1fjx: STRUCTURE OF TERNARY COMPLEX OF HHAI METHYLTRANSFERASE MUTANT (T2... -

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Basic information

Entry
Database: PDB / ID: 1fjx
TitleSTRUCTURE OF TERNARY COMPLEX OF HHAI METHYLTRANSFERASE MUTANT (T250G) IN COMPLEX WITH DNA AND ADOHCY
Components
  • DNA (5'-D(*TP*GP*AP*TP*AP*GP*CP*GP*CP*TP*AP*TP*C)-3')
  • HHAI DNA METHYLTRANSFERASE
KeywordsTRANSFERASE/DNA / AdoMet-dependent Methyltransferase fold protein-DNA-cofactor complex / TRANSFERASE-DNA COMPLEX
Function / homology
Function and homology information


DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / 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: 2.26 Å
AuthorsVilkaitis, G. / Dong, A. / Weinhold, E. / Cheng, X. / Klimasauskas, S.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: Functional roles of the conserved threonine 250 in the target recognition domain of HhaI DNA methyltransferase.
Authors: Vilkaitis, G. / Dong, A. / Weinhold, E. / Cheng, X. / Klimasauskas, S.
History
DepositionAug 8, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA (5'-D(*TP*GP*AP*TP*AP*GP*CP*GP*CP*TP*AP*TP*C)-3')
D: DNA (5'-D(*TP*GP*AP*TP*AP*GP*CP*GP*CP*TP*AP*TP*C)-3')
A: HHAI DNA METHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5086
Polymers44,9313
Non-polymers5773
Water4,234235
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.46, 98.46, 323.22
Angle α, β, γ (deg.)90, 90, 120
Int Tables number155
Space group name H-MH32
DetailsThe biological assembly is a ternary complex from HhaI Methyltransferase, a palindromic oligonucleotide, and S-adenosyl-l-homocysteine (AdoHcy)

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Components

#1: DNA chain DNA (5'-D(*TP*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 / Details: Chemically Synthesized
#2: Protein HHAI DNA METHYLTRANSFERASE


Mass: 36998.156 Da / Num. of mol.: 1 / Mutation: T250G
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
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#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.: 235 / 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: 3.33 Å3/Da / Density % sol: 63.1 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 2.7 M ammonium sulfate 20% (w/v) glucose 50 mM sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 16K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.7 Mammonium sulfate1drop
220 %(w/v)glucose1drop
350 mMsodium citrate1drop

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.26→20 Å / Num. all: 24152 / Num. obs: 67597 / % possible obs: 82.9 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 13.2
Reflection shellResolution: 2.26→2.3 Å / Rmerge(I) obs: 0.288 / Num. unique all: 474 / % possible all: 32.7
Reflection
*PLUS
Num. obs: 24152 / Num. measured all: 67597

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Processing

Software
NameVersionClassification
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.26→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.283 1896 8 %Random
Rwork0.207 ---
all-24065 --
obs-24065 82.9 %-
Refinement stepCycle: LAST / Resolution: 2.26→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3190 580 42 705 4517
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 8 % / Rfactor obs: 0.207
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONx_bond_d
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scangle_it

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