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- PDB-1u8b: Crystal structure of the methylated N-ADA/DNA complex -

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Basic information

Entry
Database: PDB / ID: 1u8b
TitleCrystal structure of the methylated N-ADA/DNA complex
Components
  • 5'-D(*AP*AP*TP*CP*TP*TP*GP*CP*GP*CP*TP*TP*T)-3'
  • 5'-D(*TP*AP*AP*AP*TP*T)-3'
  • 5'-D(P*AP*AP*AP*GP*CP*GP*CP*AP*AP*GP*AP*T)-3'
  • 5'-D(P*AP*AP*TP*TP*T)-3'
  • Ada polyprotein
KeywordsMETAL BINDING PROTEIN/DNA / PROTEIN-DNA COMPLEX / METHYLATION / ZINC / HELIX-TURN-HELIX / METAL BINDING PROTEIN-DNA COMPLEX
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 ...: / 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
DNA Methylphosphotriester Repair Domain / DNA Methylphosphotriester Repair Domain / Ada DNA repair, metal-binding / Bifunctional regulatory protein Ada / Ada-like domain superfamily / Metal binding domain of Ada / Bacterial regulatory helix-turn-helix proteins, AraC family / Methylguanine DNA methyltransferase, ribonuclease-like domain / 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain / Methylated DNA-protein cysteine methyltransferase domain superfamily ...DNA Methylphosphotriester Repair Domain / DNA Methylphosphotriester Repair Domain / Ada DNA repair, metal-binding / Bifunctional regulatory protein Ada / Ada-like domain superfamily / Metal binding domain of Ada / Bacterial regulatory helix-turn-helix proteins, AraC family / Methylguanine DNA methyltransferase, ribonuclease-like domain / 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain / Methylated DNA-protein cysteine methyltransferase domain superfamily / Methylated-DNA-[protein]-cysteine S-methyltransferase, active site / Methylated-DNA--protein-cysteine methyltransferase active site. / HTH domain AraC-type, conserved site / Bacterial regulatory proteins, araC family signature. / Methylated-DNA-[protein]-cysteine S-methyltransferase, DNA binding / Methylated DNA-protein cysteine methyltransferase, DNA binding domain / 6-O-methylguanine DNA methyltransferase, DNA binding domain / DNA binding HTH domain, AraC-type / Helix-turn-helix domain / Bacterial regulatory proteins, araC family DNA-binding domain profile. / helix_turn_helix, arabinose operon control protein / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Bifunctional transcriptional activator/DNA repair enzyme Ada
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsHe, C. / Hus, J.-C. / Sun, L.J. / Zhou, P. / Norman, D.P.G. / Dotsch, V. / Gross, J.D. / Lane, W.S. / Wagner, G. / Verdine, G.L.
CitationJournal: Mol.Cell / Year: 2005
Title: A methylation-dependent electrostatic switch controls DNA repair and transcriptional activation by E. coli ada.
Authors: He, C. / Hus, J.C. / Sun, L.J. / Zhou, P. / Norman, D.P. / Dotsch, V. / Wei, H. / Gross, J.D. / Lane, W.S. / Wagner, G. / Verdine, G.L.
History
DepositionAug 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: 5'-D(*TP*AP*AP*AP*TP*T)-3'
C: 5'-D(P*AP*AP*TP*TP*T)-3'
D: 5'-D(P*AP*AP*AP*GP*CP*GP*CP*AP*AP*GP*AP*T)-3'
E: 5'-D(*AP*AP*TP*CP*TP*TP*GP*CP*GP*CP*TP*TP*T)-3'
A: Ada polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4336
Polymers26,3685
Non-polymers651
Water1,63991
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.842, 84.593, 108.357
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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DNA chain , 4 types, 4 molecules BCDE

#1: DNA chain 5'-D(*TP*AP*AP*AP*TP*T)-3'


Mass: 1807.241 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(P*AP*AP*TP*TP*T)-3'


Mass: 1494.035 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5'-D(P*AP*AP*AP*GP*CP*GP*CP*AP*AP*GP*AP*T)-3'


Mass: 3704.457 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: DNA chain 5'-D(*AP*AP*TP*CP*TP*TP*GP*CP*GP*CP*TP*TP*T)-3'


Mass: 3932.570 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Protein , 1 types, 1 molecules A

#5: Protein Ada polyprotein


Mass: 15429.200 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ADA / Plasmid: PET30A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P06134

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Non-polymers , 2 types, 92 molecules

#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.47 Å3/Da / Density % sol: 50.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 100 mM sodium cacodylate, 100 mM NaCl, 50 mM magnesium chloride, 20% OEG 8000, pH 6.30, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium cacodylate11
2NaClSodium chloride11
3magnesium chloride11
4PEG 800011
5H2O11
6sodium cacodylate12
7NaClSodium chloride12
8magnesium chloride12
9PEG 800012
10H2O12

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793552, 0.9796687, 0.9537308
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Aug 10, 2001 / Details: MIRRORS
RadiationMonochromator: SI-111 AND SI-220 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97935521
20.97966871
30.95373081
ReflectionResolution: 2.1→39.4 Å / Num. obs: 26737 / % possible obs: 91.3 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 34.3 Å2 / Rsym value: 0.072
Reflection shellResolution: 2.1→2.18 Å / Mean I/σ(I) obs: 2.1 / Rsym value: 0.474 / % possible all: 64.7

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→39.4 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.274 999 4.7 %RANDOM
Rwork0.235 ---
obs0.235 21153 71 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.02 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 35.3 Å2
Baniso -1Baniso -2Baniso -3
1-15.32 Å20 Å20 Å2
2---4.11 Å20 Å2
3----11.2 Å2
Refinement stepCycle: LAST / Resolution: 2.1→39.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1020 699 1 91 1811
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.1→2.18 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3517 37 4.8 %
Rwork0.2828 1585 -
obs--33.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5ADA_2.PARAMADA.TOP

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