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- PDB-5cl7: Alkylpurine DNA glycosylase AlkD bound to DNA containing a 3-meth... -

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Basic information

Entry
Database: PDB / ID: 5cl7
TitleAlkylpurine DNA glycosylase AlkD bound to DNA containing a 3-methyladenine analog or DNA containing an abasic site and a free nucleobase (18% substrate/82% product at 96 hours)
Components
  • AlkD
  • DNA (5'-D(*CP*CP*CP*GP*AP*(DZM)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: 1.44 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*(DZM)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)36,0664
Polymers35,9183
Non-polymers1481
Water6,539363
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-21 kcal/mol
Surface area15030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.386, 93.153, 48.203
Angle α, β, γ (deg.)90.00, 112.81, 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*(DZM)P*AP*GP*TP*CP*CP*G)-3')


Mass: 3645.420 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.: 363 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsChain B contains microheterogeneity at position 6 (DZM versus ORP).

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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: 2.21 Å3/Da / Density % sol: 44.39 %
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: Oct 31, 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: 1.436→50 Å / Num. obs: 54698 / % possible obs: 96.4 % / Redundancy: 6.4 % / Biso Wilson estimate: 15.02 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 12.8
Reflection shellResolution: 1.44→1.46 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 3.526 / % possible all: 93.8

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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: 1.44→35.39 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 15.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.166 1999 3.66 %Random selection
Rwork0.128 ---
obs0.129 54660 96.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.63 Å2
Refinement stepCycle: LAST / Resolution: 1.44→35.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1951 499 11 363 2824
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082650
X-RAY DIFFRACTIONf_angle_d1.2193713
X-RAY DIFFRACTIONf_dihedral_angle_d18.6221026
X-RAY DIFFRACTIONf_chiral_restr0.071399
X-RAY DIFFRACTIONf_plane_restr0.008377
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4359-1.47180.21611340.15023568X-RAY DIFFRACTION92
1.4718-1.51160.19961380.12813647X-RAY DIFFRACTION94
1.5116-1.55610.161310.11643708X-RAY DIFFRACTION95
1.5561-1.60630.16231440.1133728X-RAY DIFFRACTION95
1.6063-1.66370.18511380.11043729X-RAY DIFFRACTION95
1.6637-1.73030.14131400.11073725X-RAY DIFFRACTION96
1.7303-1.80910.17311470.1123745X-RAY DIFFRACTION96
1.8091-1.90440.16651490.1163773X-RAY DIFFRACTION97
1.9044-2.02370.13791400.12373796X-RAY DIFFRACTION97
2.0237-2.180.181470.12273761X-RAY DIFFRACTION97
2.18-2.39930.14681490.12493840X-RAY DIFFRACTION98
2.3993-2.74640.17771460.13743847X-RAY DIFFRACTION98
2.7464-3.45970.18781460.13773887X-RAY DIFFRACTION99
3.4597-35.39530.15121500.13223907X-RAY DIFFRACTION99

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