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- PDB-5cl9: Alkylpurine DNA glycosylase AlkD bound to DNA containing an abasi... -

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Basic information

Entry
Database: PDB / ID: 5cl9
TitleAlkylpurine DNA glycosylase AlkD bound to DNA containing an abasic site and a free nucleobase (100% product at 240 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: 1.538 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
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-19 kcal/mol
Surface area15050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.896, 92.869, 48.492
Angle α, β, γ (deg.)90.000, 113.770, 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.: 248 / 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: 2.18 Å3/Da / Density % sol: 43.63 %
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: 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: 1.538→50 Å / Num. obs: 45394 / % possible obs: 99.5 % / Redundancy: 6.2 % / Biso Wilson estimate: 20.69 Å2 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.022 / Rrim(I) all: 0.055 / Χ2: 1.082 / Net I/av σ(I): 32 / Net I/σ(I): 14.2 / Num. measured all: 280508
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
1.538-1.574.80.5233.03221870.8990.2610.5871.11394.3
1.57-1.65.50.48222520.930.2240.5321.044100
1.6-1.635.70.42922460.9420.1950.4721.063100
1.63-1.6660.36923070.9620.1630.4041.077100
1.66-1.696.20.3222410.9750.1380.3491.085100
1.69-1.736.30.26523060.9860.1130.2881.092100
1.73-1.786.30.2322400.9880.0980.251.115100
1.78-1.836.30.18922730.9910.080.2061.152100
1.83-1.886.30.15622750.9920.0660.1691.164100
1.88-1.946.30.12822940.9950.0550.141.198100
1.94-2.016.40.10122780.9960.0430.111.23100
2.01-2.096.40.0822610.9970.0340.0871.262100
2.09-2.196.40.06322880.9980.0270.0691.043100
2.19-2.36.40.05522660.9980.0240.061.03100
2.3-2.446.40.05422810.9970.0230.0591.004100
2.44-2.636.40.06122780.9960.0260.0660.976100
2.63-2.96.40.06522810.9950.0280.0711.102100
2.9-3.326.40.05922810.9960.0250.0641.045100
3.32-4.186.40.03423130.9990.0150.0380.8999.9
4.18-506.10.02522460.9990.0110.0280.9596.3

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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: 3BVS

3bvs


Resolution: 1.538→35.02 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1864 1998 4.41 %Random selection
Rwork0.16 43354 --
obs0.1611 45352 99.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.61 Å2 / Biso mean: 32.8407 Å2 / Biso min: 14.63 Å2
Refinement stepCycle: final / Resolution: 1.538→35.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1951 477 11 248 2687
Biso mean--23.69 41.11 -
Num. residues----255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062571
X-RAY DIFFRACTIONf_angle_d0.9723587
X-RAY DIFFRACTIONf_chiral_restr0.041386
X-RAY DIFFRACTIONf_plane_restr0.006372
X-RAY DIFFRACTIONf_dihedral_angle_d17.959990
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection Rwork% reflection obs (%)
1.5377-1.57620.26791344.25530.227301597
1.5762-1.61880.24541414.3640.21353090100
1.6188-1.66640.22891424.35580.19533118100
1.6664-1.72020.21271534.71640.18353091100
1.7202-1.78170.21231374.2310.18443101100
1.7817-1.8530.19931414.37750.17753080100
1.853-1.93740.19161414.32250.17183121100
1.9374-2.03950.21551464.53280.16613075100
2.0395-2.16730.18461454.45190.16043112100
2.1673-2.33460.17991444.41850.15673115100
2.3346-2.56940.18441444.42120.16413113100
2.5694-2.94110.17951394.2690.17013117100
2.9411-3.70480.18771454.41530.15193139100
3.7048-35.02910.16631464.5440.1388306797
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)
12.7468-1.2917-1.49066.42744.122.81870.15070.0664-0.63070.2669-0.1407-0.0330.7274-0.0335-0.08510.29360.0138-0.0570.1735-0.01080.2779-24.8897-21.250421.4202
26.0024-0.62124.9513.284-1.2297.9498-0.2189-0.50290.28160.10470.12210.1944-0.2751-0.74830.08570.21490.00830.01450.2839-0.00450.2081-37.5066-7.342625.9949
39.0297-5.3213-1.81523.85213.01166.2028-0.0403-0.02670.0713-0.04110.1749-0.5525-0.01120.6411-0.15910.1921-0.03940.00850.22230.00490.219-19.7951-11.287919.6298
43.8628-1.30270.06473.53742.11435.84640.06810.3861-0.2652-0.02190.0557-0.22430.47840.1981-0.05420.27340.0046-0.03340.1861-0.03050.246-27.6585-20.52610.797
50.5368-0.40780.84770.7984-0.32753.1690.00950.0757-0.0301-0.04810.0157-0.03580.00810.1774-0.02450.1682-0.0276-0.00870.1807-0.01380.1768-34.784-10.52262.5919
64.15911.043-1.23186.0602-2.28646.38530.04660.02390.0917-0.2263-0.0729-0.3-0.28360.21870.0070.1485-0.0089-0.00470.1253-0.01680.1273-38.7322-0.2877-1.3182
72.27310.05380.56793.45760.4431.9126-0.02550.05020.1815-0.23810.0125-0.0147-0.2838-0.00740.0020.16820.01170.01220.12490.00720.1309-45.52437.0365-1.2508
82.65260.4682-0.21227.8938-0.98862.8425-0.0241-0.13660.17230.3768-0.0199-0.0207-0.29870.04180.07590.27280.01470.00340.21350.0050.2217-47.230716.56773.8262
91.4097-1.22730.29823.8035-0.12683.2279-0.3972-0.730.84440.41630.30680.1441-0.24040.0783-0.00380.38230.0786-0.05990.4707-0.12230.4636-39.92579.872218.8089
103.8466-2.07891.79323.0045-2.91142.8417-0.66470.8381.2250.55320.3327-0.4037-0.5401-0.26770.26240.43080.0849-0.02170.8176-0.21170.9478-46.881214.234719.2756
112.41262.262-1.3462.3149-1.50634.8692-0.3305-0.61940.987-0.53240.2877-1.25110.53781.0290.25010.48330.08650.12080.56130.03690.634-28.42255.652616.3614
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 53 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 54 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 206 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 207 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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