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- PDB-1m0e: ZEBULARINE: A NOVEL DNA METHYLATION INHIBITOR THAT FORMS A COVALE... -

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Basic information

Entry
Database: PDB / ID: 1m0e
TitleZEBULARINE: A NOVEL DNA METHYLATION INHIBITOR THAT FORMS A COVALENT COMPLEX WITH DNA METHYLTRANSFERASE
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*(Z)P*GP*CP*AP*TP*GP*G)-3'
  • Modification methylase HhaI
KeywordsTRANSFERASE/DNA / Protein-DNA covalent complex / Mechanism based DNA methylation inhibitors / Zebularine / 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 / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsZhou, L. / Cheng, X. / Connolly, B.A. / Dickman, M.J. / Hurd, P.J. / Hornby, D.P.
CitationJournal: J.MOL.BIOL. / Year: 2002
Title: ZEBULARINE: A NOVEL DNA METHYLATION INHIBITOR THAT FORMS A COVALENT COMPLEX WITH DNA METHYLTRANSFERASES
Authors: Zhou, L. / Cheng, X. / Connolly, B.A. / Dickman, M.J. / Hurd, P.J. / Hornby, D.P.
History
DepositionJun 12, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / struct_conn / struct_site
Item: _chem_comp.mon_nstd_flag / _chem_comp.type ..._chem_comp.mon_nstd_flag / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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*(Z)P*GP*CP*AP*TP*GP*G)-3'
A: Modification methylase HhaI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7384
Polymers44,3543
Non-polymers3841
Water4,414245
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.19, 96.19, 315.75
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-526-

HOH

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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*(Z)P*GP*CP*AP*TP*GP*G)-3'


Mass: 3688.401 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) / Production host: Escherichia coli (E. coli) / References: UniProt: P05102, EC: 2.1.1.73
#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


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.: 245 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.15 Å3/Da / Density % sol: 60.91 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, Ca acetate, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 %(w/v)PEG80001drop
2100 mMcalcium acetate1drop
350 mMsodium cacodylate1droppH6.5
450 mMsodium cacodylate1reservoirpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 16, 1999
Details: a parabolic collimating mirror placed upstream of monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→39.7 Å / Num. obs: 19591 / % possible obs: 98.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 2.5→2.61 Å / % possible all: 96.3
Reflection
*PLUS
Highest resolution: 2.5 Å

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 9MHT

9mht


Resolution: 2.5→39.7 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1938 -Random
Rwork0.177 ---
all-19591 --
obs-19591 98.1 %-
Displacement parametersBiso mean: 31.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å21.04 Å20 Å2
2--0.04 Å20 Å2
3----0.07 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å / Luzzati d res low obs: 39.7 Å / Luzzati sigma a obs: 0.26 Å
Refinement stepCycle: LAST / Resolution: 2.5→39.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2617 491 26 245 3379
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_dihedral_angle_d26.2
X-RAY DIFFRACTIONx_improper_angle_d1.47
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.019
RfactorNum. reflection% reflection
Rfree0.329 312 -
Rwork0.268 --
obs--96.3 %
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rfree: 0.243 / Rfactor Rwork: 0.177
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.47
LS refinement shell
*PLUS
Rfactor Rfree: 0.329 / Rfactor Rwork: 0.268

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