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

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Basic information

Entry
Database: PDB / ID: 5cla
TitleAlkylpurine DNA glycosylase AlkD bound to DNA containing an abasic site and a free nucleobase (100% product at 360 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: 1.541 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*(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
Water7,206400
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-19 kcal/mol
Surface area14990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.427, 93.082, 48.045
Angle α, β, γ (deg.)90.000, 112.610, 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*(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.: 400 / 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: 2.22 Å3/Da / Density % sol: 44.51 %
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-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 15, 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: 44689 / % possible obs: 96.9 % / Redundancy: 7.7 % / Biso Wilson estimate: 13.69 Å2 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.019 / Rrim(I) all: 0.053 / Χ2: 1.351 / Net I/av σ(I): 41.066 / Net I/σ(I): 20.9 / Num. measured all: 344562
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
1.54-1.67.40.13816.59442310.9940.0540.1491.17192.3
1.6-1.667.60.1144200.9950.0430.1181.25296.2
1.66-1.737.70.08944290.9960.0350.0961.35996.6
1.73-1.837.70.07544550.9970.0290.0811.44596.6
1.83-1.947.80.06544730.9970.0250.071.64197.1
1.94-2.097.80.05544870.9980.0210.0581.52497.6
2.09-2.37.80.0544950.9980.0190.0541.36397.9
2.3-2.637.80.04945360.9980.0190.0531.21398.4
2.63-3.327.80.04845790.9980.0180.0511.37898.9
3.32-507.60.04345840.9980.0170.0461.14697.5

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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→35.043 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 16.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1694 1997 4.47 %Random selection
Rwork0.148 42654 --
obs0.149 44651 97.11 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.7 Å2 / Biso mean: 21.8958 Å2 / Biso min: 8.02 Å2
Refinement stepCycle: final / Resolution: 1.541→35.043 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1951 477 11 400 2839
Biso mean--13.61 33.51 -
Num. residues----255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062587
X-RAY DIFFRACTIONf_angle_d1.0413614
X-RAY DIFFRACTIONf_chiral_restr0.043390
X-RAY DIFFRACTIONf_plane_restr0.006376
X-RAY DIFFRACTIONf_dihedral_angle_d17.9861001
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection Rwork% reflection obs (%)
1.5407-1.57920.19351324.34640.1472290594
1.5792-1.62190.16141434.51530.1474302496
1.6219-1.66970.14771384.35060.1419303496
1.6697-1.72360.19221414.49620.1404299597
1.7236-1.78520.18421474.66370.1464300596
1.7852-1.85660.16711364.27540.1511304597
1.8566-1.94110.18391494.64460.1509305997
1.9411-2.04340.19351444.51980.1546304297
2.0434-2.17150.16951414.41310.1519305498
2.1715-2.33910.15831494.63310.1508306798
2.3391-2.57440.19291444.42670.1592310998
2.5744-2.94680.17231454.48360.1638308999
2.9468-3.7120.17521494.5510.1465312599
3.712-35.05190.13951394.29010.1321310197
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)
11.3727-0.77830.62174.5034-3.58474.58960.05250.01340.33790.145-0.0736-0.0486-0.54750.045-0.00590.19620.00320.0390.1229-0.00050.167745.599721.105265.967
22.5292-0.2961-2.0991.78650.91523.5394-0.0723-0.2636-0.06390.05620.086-0.10120.03990.3705-0.00410.09430.0048-0.01780.14510.0010.101758.10967.139570.5412
32.8221-0.90150.58123.6261-2.19963.96590.13310.08560.0529-0.09920.10120.4318-0.1169-0.2654-0.22980.12730.0022-0.01370.13980.00230.139640.029812.893862.2583
43.1663-1.22782.67343.0982-2.15596.3508-0.07470.11480.2230.06330.01480.0122-0.49180.08880.09250.1351-0.00670.02120.08660.01070.11950.540120.45255.6502
50.4178-0.2849-0.40270.59530.30251.57470.0250.05040.0096-0.04790.00750.0379-0.0603-0.0971-0.0340.1043-0.0127-0.00160.10570.00560.102855.48610.434147.1408
62.27820.55320.84983.40871.5364.18110.03640.0063-0.0953-0.1259-0.01640.14930.1398-0.1429-0.01430.0855-0.01-0.00370.07340.01560.07859.32130.225343.1597
73.10260.1930.04292.60850.24182.75790.09070.1696-0.0694-0.17410.0068-0.05070.19510.1904-0.11560.08220.00870.00470.052-0.00620.064969.8903-1.789641.1275
80.9078-0.0857-0.1422.1230.59551.0622-0.0524-0.0387-0.1592-0.00250.02840.02440.18450.0210.02150.1491-0.01110.00490.0984-0.00320.11565.513-13.016346.0382
90.11-0.3293-0.29162.0543-0.05191.5732-0.2456-0.5044-0.49940.20330.1302-0.08030.1628-0.1287-0.04650.16190.03580.02660.27360.0820.248460.3588-9.949563.2229
104.4537-0.7421-0.50751.46250.62520.2763-0.15930.2275-0.57910.09050.12680.01850.09550.1452-0.03790.22630.07350.07650.57210.25290.580967.5415-14.380663.7519
113.44631.8899-0.73315.6597-0.08312.1859-0.39450.0737-0.5606-0.30450.1951.0278-0.4532-0.64370.1640.22930.1108-0.02990.3813-0.02790.326648.9857-5.6960.6956
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 143 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 144 through 162 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 163 through 178 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 179 through 229 )A0
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 12 )B0
10X-RAY DIFFRACTION10chain 'C' and (resid 1 through 6 )C0
11X-RAY DIFFRACTION11chain 'C' and (resid 7 through 12 )C0

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