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- PDB-3jxy: Bacillus cereus Alkylpurine DNA Glycosylase AlkD Bound to DNA Con... -

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Basic information

Entry
Database: PDB / ID: 3jxy
TitleBacillus cereus Alkylpurine DNA Glycosylase AlkD Bound to DNA Containing a GT Mismatch
Components
  • DNA (5'-D(*CP*CP*CP*GP*TP*TP*AP*GP*TP*CP*CP*G)-3')
  • DNA (5'-D(*CP*GP*GP*AP*CP*TP*GP*AP*CP*GP*GP*G)-3')
  • alkylpurine DNA glycosylase AlkD
Keywordshydrolase/DNA / HEAT repeat / DNA binding / DNA glycosylase / DNA alkylation / lyase-DNA COMPLEX / hydrolase-DNA COMPLEX
Function / homology
Function and homology information


Leucine-rich Repeat Variant - #90 / DNA alkylation repair enzyme / DNA alkylation repair enzyme / Leucine-rich Repeat Variant / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA alkylation repair protein
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsRubinson, E.H. / Eichman, B.F.
CitationJournal: Nature / Year: 2010
Title: An unprecedented nucleic acid capture mechanism for excision of DNA damage.
Authors: Rubinson, E.H. / Gowda, A.S. / Spratt, T.E. / Gold, B. / Eichman, B.F.
History
DepositionSep 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: alkylpurine DNA glycosylase AlkD
B: DNA (5'-D(*CP*GP*GP*AP*CP*TP*GP*AP*CP*GP*GP*G)-3')
C: DNA (5'-D(*CP*CP*CP*GP*TP*TP*AP*GP*TP*CP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)35,0673
Polymers35,0673
Non-polymers00
Water9,458525
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-16 kcal/mol
Surface area15120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.200, 93.594, 48.118
Angle α, β, γ (deg.)90.00, 112.60, 90.00
Int Tables number4
Space group name H-MP1211
Detailsbiological unit is asymmetric unit

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Components

#1: Protein alkylpurine DNA glycosylase AlkD


Mass: 27724.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 10987 / Gene: AlkD, BC_4913 / Plasmid: pBG103 / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 / References: UniProt: Q816E8
#2: DNA chain DNA (5'-D(*CP*GP*GP*AP*CP*TP*GP*AP*CP*GP*GP*G)-3')


Mass: 3728.429 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*CP*CP*CP*GP*TP*TP*AP*GP*TP*CP*CP*G)-3')


Mass: 3614.354 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 525 / 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: 2.26 Å3/Da / Density % sol: 45.69 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M BisTris pH 5.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9785 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 11, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.5→35.3 Å / Num. all: 49763 / Num. obs: 46379 / % possible obs: 93.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 17.2 Å2 / Rsym value: 0.043 / Net I/σ(I): 22
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 4.9 / Rsym value: 0.186 / % possible all: 87.2

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 3JX7

3jx7


Resolution: 1.5→28.164 Å / SU ML: 0.17 / σ(F): 1.42 / Phase error: 16.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1735 2374 5.12 %
Rwork0.1304 --
obs0.1326 46341 92.94 %
all-46351 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.521 Å2 / ksol: 0.404 e/Å3
Displacement parametersBiso mean: 24.2 Å2
Refinement stepCycle: LAST / Resolution: 1.5→28.164 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1945 487 0 525 2957
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052552
X-RAY DIFFRACTIONf_angle_d0.9863558
X-RAY DIFFRACTIONf_dihedral_angle_d19.906975
X-RAY DIFFRACTIONf_chiral_restr0.066384
X-RAY DIFFRACTIONf_plane_restr0.004366
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5001-1.53070.20541220.10752332X-RAY DIFFRACTION83
1.5307-1.5640.18551260.10112392X-RAY DIFFRACTION87
1.564-1.60040.19791290.09952446X-RAY DIFFRACTION88
1.6004-1.64040.19421140.09712478X-RAY DIFFRACTION89
1.6404-1.68470.17481410.09412479X-RAY DIFFRACTION89
1.6847-1.73430.15821290.09712535X-RAY DIFFRACTION90
1.7343-1.79030.17891530.09842510X-RAY DIFFRACTION91
1.7903-1.85430.17621480.10732541X-RAY DIFFRACTION92
1.8543-1.92850.18221430.10592588X-RAY DIFFRACTION93
1.9285-2.01620.16511330.10792646X-RAY DIFFRACTION94
2.0162-2.12250.17091610.10832622X-RAY DIFFRACTION95
2.1225-2.25540.16321570.10542669X-RAY DIFFRACTION97
2.2554-2.42950.15811290.1122735X-RAY DIFFRACTION98
2.4295-2.67380.16721420.12232750X-RAY DIFFRACTION98
2.6738-3.06030.16691460.12022733X-RAY DIFFRACTION98
3.0603-3.85410.12661410.11442774X-RAY DIFFRACTION98
3.8541-28.1690.17741600.15912737X-RAY DIFFRACTION97

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