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

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Basic information

Entry
Database: PDB / ID: 5clb
TitleAlkylpurine DNA glycosylase AlkD bound to DNA containing a 3-methyladenine analog (9-mer A)
Components
  • AlkD
  • DNA (5'-D(*AP*AP*GP*CP*AP*(DZM)P*AP*CP*C)-3')
  • DNA (5'-D(*TP*GP*GP*TP*TP*TP*GP*CP*T)-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
DNA / 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: 1.766 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 6, 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(*AP*AP*GP*CP*AP*(DZM)P*AP*CP*C)-3')
C: DNA (5'-D(*TP*GP*GP*TP*TP*TP*GP*CP*T)-3')


Theoretical massNumber of molelcules
Total (without water)34,0623
Polymers34,0623
Non-polymers00
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-16 kcal/mol
Surface area13550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.439, 55.405, 47.969
Angle α, β, γ (deg.)90.000, 105.700, 90.000
Int Tables number5
Space group name H-MC121

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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(*AP*AP*GP*CP*AP*(DZM)P*AP*CP*C)-3')


Mass: 2730.866 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*GP*GP*TP*TP*TP*GP*CP*T)-3')


Mass: 2752.806 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.39 Å3/Da / Density % sol: 48.6 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 22% w/v PEG8000, 50 mM HEPES, pH 7.0, 50 mM calcium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 18, 2015
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.766→50 Å / Num. obs: 30648 / % possible obs: 96.7 % / Redundancy: 4.6 % / Biso Wilson estimate: 18.17 Å2 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.045 / Rrim(I) all: 0.099 / Χ2: 1.024 / Net I/av σ(I): 14.977 / Net I/σ(I): 9 / Num. measured all: 139873
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.766-1.834.20.4142.7225340.8610.220.4711.00980
1.83-1.914.30.37528430.8840.2020.4281.04390.5
1.91-1.994.50.30730480.9310.1640.351.06396.6
1.99-2.14.60.2431290.9550.1270.2721.11999.6
2.1-2.234.70.17131520.9770.090.1931.104100
2.23-2.44.70.12931790.9860.0670.1451.021100
2.4-2.644.70.09831560.9910.0510.1110.905100
2.64-3.034.70.08531690.9930.0430.0951.019100
3.03-3.814.70.07531710.9950.0370.0841.144100
3.81-504.60.0432670.9980.0210.0460.81899.9

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Processing

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

3bvs


Resolution: 1.766→46.18 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2032 1533 5 %Random selection
Rwork0.1633 29105 --
obs0.1653 30638 96.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.35 Å2 / Biso mean: 27.2419 Å2 / Biso min: 8.87 Å2
Refinement stepCycle: final / Resolution: 1.766→46.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1898 364 0 253 2515
Biso mean---34.04 -
Num. residues----242
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072361
X-RAY DIFFRACTIONf_angle_d1.033272
X-RAY DIFFRACTIONf_chiral_restr0.044350
X-RAY DIFFRACTIONf_plane_restr0.006351
X-RAY DIFFRACTIONf_dihedral_angle_d18.597898
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection Rwork% reflection obs (%)
1.766-1.8230.276711050.2278209077
1.823-1.88820.25461295.02140.2122244090
1.8882-1.96370.23861374.99810.2025260496
1.9637-2.05310.25651434.98430.202272699
2.0531-2.16140.20361434.99650.1712719100
2.1614-2.29680.22011444.99830.16082737100
2.2968-2.47410.21821445.0420.15692712100
2.4741-2.72310.18671444.98960.1722742100
2.7231-3.1170.21241444.98440.16232745100
3.117-3.92680.16491465.00510.14852771100
3.9268-46.19540.18911495.02020.14132819100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.68172.010.86526.07450.95420.94370.0934-0.13160.45310.2087-0.19080.7816-0.0422-0.68490.10620.13-0.0330.03930.4505-0.03790.234-3.994831.832516.7795
23.2631-1.7372-1.98790.92581.03021.53070.6148-0.63341.22620.3135-0.19050.2073-0.75110.0504-0.4910.3911-0.02670.19530.308-0.150.4410.613945.544818.9674
35.02060.6476-1.46783.7438-1.63745.40870.1688-0.35020.25610.19-0.15540.0594-0.0961-0.0901-0.01350.14420.02380.02140.194-0.05970.15278.097235.299718.4624
43.98380.1182-0.58783.72210.52313.63750.01510.2624-0.20740.20370.07620.51860.3993-0.7652-0.12430.1819-0.07740.02610.4389-0.02680.20930.408125.32219.851
52.1334-0.1449-1.08353.28372.34343.21720.0327-0.076-0.16940.3565-0.18580.14240.363-0.24540.15470.1459-0.02840.01270.21490.01560.16828.595123.39837.4922
62.1327-1.4279-0.30983.74291.17092.41610.0325-0.0491-0.04420.04450.01070.1418-0.0005-0.0951-0.03560.0823-0.0225-0.01190.13280.00460.118517.461324.33110.2841
74.3481-4.12671.66325.7142-1.63851.1026-0.0564-0.0303-0.12930.14470.07880.1027-0.049-0.0528-0.03460.1096-0.0123-0.00450.0919-0.00670.090224.782823.88522.7488
81.51880.02780.43042.8975-0.9542.38310.00610.0357-0.02240.043-0.0606-0.1691-0.00250.18060.02750.0785-0.0080.00080.0779-0.01080.101933.572328.03690.1384
95.9879-1.92151.5475.7063-0.39617.6610.0381-0.48460.1110.5077-0.0412-0.4899-0.20010.19350.04410.1306-0.0549-0.02290.10240.02530.17640.125432.88344.6819
104.0941.0462-0.23345.377-2.12026.50930.1523-0.8118-0.37710.9123-0.08110.22890.17240.4108-0.13760.36280.00160.0340.31180.05930.231727.09134.027717.6214
115.42061.385-1.4733.8432-1.46053.59340.1269-0.7855-0.2680.3422-0.47330.31730.060.16930.22890.3648-0.04090.05580.2613-0.01280.257326.474338.074118.6222
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 15 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 27 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 28 through 50 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 51 through 73 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 74 through 104 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 105 through 143 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 144 through 162 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 163 through 206 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 207 through 225 )A0
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 9 )B0
11X-RAY DIFFRACTION11chain 'C' and (resid 1 through 9 )C0

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