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- PDB-5cl6: Alkylpurine DNA glycosylase AlkD bound to DNA containing a 3-meth... -

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Basic information

Entry
Database: PDB / ID: 5cl6
TitleAlkylpurine DNA glycosylase AlkD bound to DNA containing a 3-methyladenine analog or DNA containing an abasic site and a free nucleobase (33% substrate/67% product at 72 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: 1.541 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
Water7,440413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-21 kcal/mol
Surface area15000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.389, 93.282, 48.077
Angle α, β, γ (deg.)90.000, 112.720, 90.000
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 / Water


Mass: 18.015 Da / Num. of mol.: 413 / 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: 44.36 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 17% 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-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 2, 2014
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.54→50 Å / Num. obs: 45888 / % possible obs: 99.4 % / Redundancy: 7.5 % / Biso Wilson estimate: 15.52 Å2 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.023 / Rrim(I) all: 0.062 / Χ2: 1.241 / Net I/av σ(I): 33.965 / Net I/σ(I): 19 / Num. measured all: 342664
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.54-1.576.80.18410.26221560.9880.0750.1990.9593.9
1.57-1.67.40.16723150.9920.0660.1790.97999.9
1.6-1.637.40.14822610.9910.0580.1591.00999.7
1.63-1.667.40.12523050.9940.0490.1351.04599.9
1.66-1.697.40.11323000.9950.0450.1221.1599.9
1.69-1.737.50.10123210.9960.040.1091.173100
1.73-1.787.40.09122700.9970.0360.0981.232100
1.78-1.837.50.08323150.9950.0330.091.289100
1.83-1.887.50.07622780.9970.030.0821.39499.8
1.88-1.947.50.0723370.9970.0270.0751.482100
1.94-2.017.50.06522880.9960.0250.0691.463100
2.01-2.097.50.05823100.9980.0230.0621.305100
2.09-2.197.60.05723100.9980.0220.0611.175100
2.19-2.37.60.05322900.9980.0210.0571.406100
2.3-2.447.70.05523190.9980.0210.0591.298100
2.44-2.637.70.06122950.9970.0240.0661.355100
2.63-2.97.70.0723090.9960.0270.0751.539100
2.9-3.327.60.06623140.9960.0260.0711.058100
3.32-4.187.50.04923390.9970.0190.0521.45499.9
4.18-507.20.04422560.9970.0180.0480.96495.2

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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: 1.541→35.048 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 18.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1828 2006 4.38 %Random selection
Rwork0.1531 43840 --
obs0.1544 45846 99.58 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.12 Å2 / Biso mean: 24.3502 Å2 / Biso min: 9.92 Å2
Refinement stepCycle: final / Resolution: 1.541→35.048 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1951 499 11 413 2874
Biso mean--15.48 35.23 -
Num. residues----255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062647
X-RAY DIFFRACTIONf_angle_d1.0433709
X-RAY DIFFRACTIONf_chiral_restr0.042399
X-RAY DIFFRACTIONf_plane_restr0.006375
X-RAY DIFFRACTIONf_dihedral_angle_d18.6811024
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection Rwork% reflection obs (%)
1.5407-1.57920.21061414.37340.1692308399
1.5792-1.62190.18291484.51770.16263128100
1.6219-1.66960.191394.2160.14953158100
1.6696-1.72350.1871474.5120.14693111100
1.7235-1.78510.1791414.31990.14853123100
1.7851-1.85660.1771434.36910.15543130100
1.8566-1.94110.17881404.25920.15753147100
1.9411-2.04340.19841434.37040.16683129100
2.0434-2.17140.19221404.26570.15593142100
2.1714-2.3390.18421464.44440.15623139100
2.339-2.57430.18191444.34780.16283168100
2.5743-2.94670.18681454.42070.1633135100
2.9467-3.71180.18851444.35970.14973159100
3.7118-35.0570.16531454.4850.1379308897
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)
11.7354-0.50620.33945.5781-4.86915.73230.0747-0.00760.33860.1049-0.05950.0356-0.5252-0.0367-0.03630.2274-0.00150.03510.1392-0.01160.188945.524821.096565.7336
24.0891-0.4912-3.65462.41191.145.5541-0.1251-0.3185-0.10310.07360.0758-0.11250.12420.44110.04230.12390.0013-0.02140.16120.00130.129757.87057.077270.5474
33.8906-1.21830.93444.9237-2.55895.08030.12280.06960.0189-0.02410.07510.4632-0.1203-0.3131-0.18820.1228-0.0061-0.01760.1381-0.0120.124139.83812.914462.2239
44.2005-1.39434.07083.6511-2.72528.3266-0.11460.13540.26630.03630.00990.0693-0.5330.12260.1330.1751-0.00940.0340.0996-0.00130.145450.399520.46755.6852
50.6234-0.4057-0.38040.63810.4932.21920.02940.0314-0.008-0.02390.00630.0327-0.0554-0.0919-0.03650.1215-0.0241-0.00210.11260.00610.119856.15668.14746.2773
61.44440.4078-0.55192.25390.11231.1299-0.04390.0074-0.1049-0.11250.00860.04420.16810.00270.03040.1237-0.0059-0.0040.0857-0.00690.094365.8614-7.089443.3122
71.37110.75020.63736.31311.05372.23350.0227-0.101-0.01970.3963-0.03010.13250.2793-0.04380.02270.18750.0030.01160.1527-0.00060.136767.3097-16.892848.0631
80.1443-0.4153-0.48342.76970.45272.188-0.2924-0.6095-0.60450.21720.1776-0.08940.1307-0.15880.02780.21010.03850.04160.31660.08670.306259.9684-9.607862.7889
96.7416-0.53270.11162.74070.74360.235-0.24880.289-0.67010.18450.19340.1480.11690.249-0.09790.24180.08060.06390.60540.29310.607666.0967-13.953364.4962
106.20962.4126-0.67678.55242.0954.4221-0.3622-0.3236-0.6251-0.42320.27940.699-0.7669-0.83660.04470.230.1201-0.00080.36060.00420.296649.8411-5.950162.224
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 38 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 39 through 57 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 58 through 73 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 74 through 162 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 163 through 206 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 207 through 229 )A0
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 12 )B0
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 6 )C0
10X-RAY DIFFRACTION10chain 'C' and (resid 7 through 12 )C0

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