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- PDB-5cl8: Alkylpurine DNA glycosylase AlkD bound to DNA containing an abasi... -

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Basic information

Entry
Database: PDB / ID: 5cl8
TitleAlkylpurine DNA glycosylase AlkD bound to DNA containing an abasic site and a free nucleobase (100% product at 144 hours)
Components
  • AlkD
  • DNA (5'-D(*CP*CP*CP*GP*AP*(ORP)P*AP*GP*TP*CP*CP*G)-3')
  • DNA (5'-D(*CP*GP*GP*AP*CP*TP*TP*TP*CP*GP*GP*G)-3')
KeywordsHYDROLASE/DNA / DNA glycosylase / HEAT-like repeat / protein-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
7-methyl-3H-imidazo[4,5-c]pyridin-4-amine / DNA / DNA (> 10) / DNA alkylation repair protein / DNA alkylation repair enzyme
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsMullins, E.A. / Eichman, B.F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1122098 United States
CitationJournal: Nature / Year: 2015
Title: The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions.
Authors: Mullins, E.A. / Shi, R. / Parsons, Z.D. / Yuen, P.K. / David, S.S. / Igarashi, Y. / Eichman, B.F.
History
DepositionJul 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Database references
Revision 1.2Nov 25, 2015Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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: AlkD
B: DNA (5'-D(*CP*CP*CP*GP*AP*(ORP)P*AP*GP*TP*CP*CP*G)-3')
C: DNA (5'-D(*CP*GP*GP*AP*CP*TP*TP*TP*CP*GP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9364
Polymers35,7883
Non-polymers1481
Water7,296405
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-18 kcal/mol
Surface area15070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.502, 93.446, 48.767
Angle α, β, γ (deg.)90.00, 114.19, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein AlkD


Mass: 28578.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: IKE_03968 / Plasmid: pBG103 / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174
References: UniProt: R8GWR7, UniProt: Q816E8*PLUS, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: DNA chain DNA (5'-D(*CP*CP*CP*GP*AP*(ORP)P*AP*GP*TP*CP*CP*G)-3')


Mass: 3515.270 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*CP*GP*GP*AP*CP*TP*TP*TP*CP*GP*GP*G)-3')


Mass: 3694.402 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-54K / 7-methyl-3H-imidazo[4,5-c]pyridin-4-amine / 3-deaza-3-methyladenine


Mass: 148.165 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / 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: 2.24 Å3/Da / Density % sol: 44.99 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 15% w/v PEG4000, 42 mM sodium acetate, pH 4.6, 85 mM ammonium acetate, 5% v/v glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 25, 2014
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.38→50 Å / Num. obs: 64201 / % possible obs: 99.5 % / Redundancy: 7.3 % / Biso Wilson estimate: 14.62 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 17.1
Reflection shellResolution: 1.38→1.4 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 5.091 / % possible all: 96.1

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Processing

Software
NameClassification
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BVS

3bvs


Resolution: 1.38→35.12 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.158 2004 3.13 %Random selection
Rwork0.133 ---
obs0.134 64110 99.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.89 Å2
Refinement stepCycle: LAST / Resolution: 1.38→35.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1951 477 11 405 2844
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082586
X-RAY DIFFRACTIONf_angle_d1.1573611
X-RAY DIFFRACTIONf_dihedral_angle_d18.3631000
X-RAY DIFFRACTIONf_chiral_restr0.065389
X-RAY DIFFRACTIONf_plane_restr0.007377
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3796-1.41410.23081360.16014266X-RAY DIFFRACTION96
1.4141-1.45240.18561370.13894420X-RAY DIFFRACTION100
1.4524-1.49510.16941460.12474443X-RAY DIFFRACTION100
1.4951-1.54340.16291380.11154463X-RAY DIFFRACTION100
1.5434-1.59850.16191450.1114472X-RAY DIFFRACTION100
1.5985-1.66250.16821440.11164437X-RAY DIFFRACTION100
1.6625-1.73820.1571430.11374456X-RAY DIFFRACTION100
1.7382-1.82980.15381430.12174463X-RAY DIFFRACTION100
1.8298-1.94440.17181470.12484461X-RAY DIFFRACTION100
1.9444-2.09460.16921460.1294442X-RAY DIFFRACTION100
2.0946-2.30530.1411440.12784463X-RAY DIFFRACTION100
2.3053-2.63880.1491450.13684467X-RAY DIFFRACTION100
2.6388-3.32420.16741460.14324464X-RAY DIFFRACTION100
3.3242-35.13280.14721440.14164389X-RAY DIFFRACTION97

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