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- PDB-1sfe: ADA O6-METHYLGUANINE-DNA METHYLTRANSFERASE FROM ESCHERICHIA COLI -

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Basic information

Entry
Database: PDB / ID: 1sfe
TitleADA O6-METHYLGUANINE-DNA METHYLTRANSFERASE FROM ESCHERICHIA COLI
ComponentsADA O6-METHYLGUANINE-DNA METHYLTRANSFERASE
KeywordsDNA BINDING PROTEIN / ENZYME / TRANSFERASE / METHYLTRANSFERASE / NUCLEIC ACID BINDING PROTEIN / DNA REPAIR PROTEIN / DNA-BINDING PROTEIN
Function / homology
Function and homology information


: / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / DNA alkylation repair / methylation / sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA damage response / positive regulation of DNA-templated transcription / zinc ion binding
Similarity search - Function
Ada DNA repair, metal-binding / Bifunctional regulatory protein Ada / Ada-like domain superfamily / Metal binding domain of Ada / Methylated DNA-protein cysteine methyltransferase domain / HTH domain AraC-type, conserved site / Bacterial regulatory proteins, araC family signature. / Methylguanine DNA methyltransferase, ribonuclease-like domain / 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain / Helix-turn-helix domain ...Ada DNA repair, metal-binding / Bifunctional regulatory protein Ada / Ada-like domain superfamily / Metal binding domain of Ada / Methylated DNA-protein cysteine methyltransferase domain / HTH domain AraC-type, conserved site / Bacterial regulatory proteins, araC family signature. / Methylguanine DNA methyltransferase, ribonuclease-like domain / 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain / Helix-turn-helix domain / Methylated DNA-protein cysteine methyltransferase domain superfamily / Methylated-DNA-[protein]-cysteine S-methyltransferase, active site / Methylated-DNA--protein-cysteine methyltransferase active site. / DNA binding HTH domain, AraC-type / Bacterial regulatory proteins, araC family DNA-binding domain profile. / helix_turn_helix, arabinose operon control protein / Methylated-DNA-[protein]-cysteine S-methyltransferase, DNA binding / Methylated DNA-protein cysteine methyltransferase, DNA binding domain / 6-O-methylguanine DNA methyltransferase, DNA binding domain / Double Stranded RNA Binding Domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Bifunctional transcriptional activator/DNA repair enzyme Ada
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsMoore, M.H. / Gulbis, J.M. / Dodson, E.J. / Demple, B. / Moody, P.C.E.
Citation
Journal: EMBO J. / Year: 1994
Title: Crystal structure of a suicidal DNA repair protein: the Ada O6-methylguanine-DNA methyltransferase from E. coli.
Authors: Moore, M.H. / Gulbis, J.M. / Dodson, E.J. / Demple, B. / Moody, P.C.
#1: Journal: Novel Approaches in Anticancer Drug Design : Molecular Modelling--New Treatment Strategies (in: Contrib.Oncol., V.49)
Year: 1995
Title: Crystal Structure of E.Coli O6-Methylguanine-DNA Methyltransferase
Authors: Moody, P.C.E. / Moore, M.H.
#2: Journal: J.Mol.Biol. / Year: 1988
Title: Crystallization of O6-Methylguanine-DNA Methyltransferase from Escherichia Coli
Authors: Moody, P.C. / Demple, B.
History
DepositionJun 21, 1996Processing site: BNL
Revision 1.0Dec 23, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_keywords
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADA O6-METHYLGUANINE-DNA METHYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)19,7671
Polymers19,7671
Non-polymers00
Water2,612145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.200, 45.950, 46.400
Angle α, β, γ (deg.)90.00, 114.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ADA O6-METHYLGUANINE-DNA METHYLTRANSFERASE


Mass: 19766.586 Da / Num. of mol.: 1 / Fragment: C-TERMINAL 19KD OF THE ADA PROTEIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: B / Description: TAC CONTROL / Gene: ADAC / Variant: JM 101 / Plasmid: PADAC / Gene (production host): ADAC / Production host: Escherichia coli (E. coli)
References: UniProt: P06134, methylated-DNA-[protein]-cysteine S-methyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 48 %
Crystal
*PLUS
Crystal grow
*PLUS
Method: microdialysis / PH range low: 8 / PH range high: 7.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15-50 mg/mlprotein11
2200-500 mMsodium acetate11
310 mMdithiothreitol11
410-20 mMTris-acetate11
510 mMdithiothreitol12
6300 mMglucose12can be replaced by maltose
710 mMTris-acetate12

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Data collection

Diffraction
IDCrystal-ID
11
21
1,21
Diffraction source
SourceSiteBeamlineTypeIDWavelength
SYNCHROTRONPhoton Factory BL-6A10.89
ROTATING ANODERIGAKU RU30020.707
Detector
TypeIDDetector
WEISSENBERG1DIFFRACTOMETER
RIGAKU2IMAGE PLATE
Radiation
IDMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Mx-ray1
2Mx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.891
20.7071
ReflectionNum. obs: 9017 / % possible obs: 86 % / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Rmerge(I) obs: 0.058
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 40 Å / Num. measured all: 19437

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Processing

Software
NameClassification
PROLSQrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.1→39 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.219 -
all-9017
obs-9017
Displacement parametersBiso mean: 44.9 Å2
Refine analyzeLuzzati sigma a obs: 0.15 Å
Refinement stepCycle: LAST / Resolution: 2.1→39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1257 0 0 145 1402
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.02
X-RAY DIFFRACTIONp_angle_d0.0310.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0330.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.5922
X-RAY DIFFRACTIONp_mcangle_it2.593
X-RAY DIFFRACTIONp_scbond_it1.5972
X-RAY DIFFRACTIONp_scangle_it2.583
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.1120.15
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.97
X-RAY DIFFRACTIONp_staggered_tor22.315
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor41.420
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.219
Solvent computation
*PLUS
Displacement parameters
*PLUS

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