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- PDB-5cld: Alkylpurine DNA glycosylase AlkD bound to DNA containing an oxoca... -

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Basic information

Entry
Database: PDB / ID: 5cld
TitleAlkylpurine DNA glycosylase AlkD bound to DNA containing an oxocarbenium-intermediate analog and a free 3-methyladenine nucleobase
Components
  • AlkD
  • DNA (5'-D(*CP*CP*CP*GP*AP*(NRI)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
3-METHYL-3H-PURIN-6-YLAMINE / 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*(NRI)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)35,9204
Polymers35,7713
Non-polymers1491
Water7,476415
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-11 kcal/mol
Surface area14910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.202, 92.826, 48.309
Angle α, β, γ (deg.)90.000, 113.710, 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*(NRI)P*AP*GP*TP*CP*CP*G)-3')


Mass: 3498.286 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-ADK / 3-METHYL-3H-PURIN-6-YLAMINE / 3-METHYLADENINE


Mass: 149.153 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H7N5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / 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: 2.19 Å3/Da / Density % sol: 43.9 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 19% 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: 44235 / % possible obs: 97.2 % / Redundancy: 7.1 % / Biso Wilson estimate: 12.96 Å2 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.023 / Rrim(I) all: 0.062 / Χ2: 1.195 / Net I/av σ(I): 26.213 / Net I/σ(I): 14.9 / Num. measured all: 313407
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
1.54-1.576.40.2556.90220710.9720.1050.2770.93592.2
1.57-1.66.80.23221830.9780.0930.2510.97595.3
1.6-1.6370.20921370.9780.0840.2251.04395.6
1.63-1.666.80.18421960.9850.0730.1981.11594.9
1.66-1.696.90.1621480.9860.0640.1721.2196.8
1.69-1.736.80.14622040.9880.0590.1581.27795.5
1.73-1.786.90.13321630.9910.0530.1431.36396.3
1.78-1.836.80.11822030.9910.0480.1281.42797.3
1.83-1.886.90.10721830.9930.0430.1161.55496.8
1.88-1.946.90.09922250.9930.040.1071.65396.9
1.94-2.016.80.08922480.9940.0360.0961.53997.4
2.01-2.0970.0821910.9950.0320.0861.60898.2
2.09-2.197.10.07122380.9960.0290.0771.2798.3
2.19-2.37.20.06722270.9960.0270.0721.11798.4
2.3-2.447.30.06122520.9970.0240.0651.24599.2
2.44-2.637.50.06122510.9970.0240.0651.14599.4
2.63-2.97.70.0622730.9970.0230.0641.1299.2
2.9-3.327.70.05322660.9980.0210.0571.08199.6
3.32-4.187.70.0423090.9990.0150.0430.79399.8
4.18-507.40.03622670.9990.0140.0380.58197.5

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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→34.979 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 16.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1792 1997 4.52 %Random selection
Rwork0.1494 42197 --
obs0.1508 44194 97.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.54 Å2 / Biso mean: 20.2579 Å2 / Biso min: 6.57 Å2
Refinement stepCycle: final / Resolution: 1.541→34.979 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1951 476 11 415 2853
Biso mean--19.59 31.92 -
Num. residues----255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062575
X-RAY DIFFRACTIONf_angle_d1.0493594
X-RAY DIFFRACTIONf_chiral_restr0.043387
X-RAY DIFFRACTIONf_plane_restr0.006373
X-RAY DIFFRACTIONf_dihedral_angle_d18.008995
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection Rwork% reflection obs (%)
1.5407-1.57930.17931374.5470.153287693
1.5793-1.6220.19891374.49030.151291495
1.622-1.66970.20341394.42960.1537299995
1.6697-1.72360.18561424.60290.151294396
1.7236-1.78520.17961374.41080.1467296996
1.7852-1.85660.17721364.32980.1515300597
1.8566-1.94110.1751444.54690.1515302398
1.9411-2.04350.16491444.58160.1591299998
2.0435-2.17150.18981494.65480.1455305298
2.1715-2.33910.18471464.55540.1463305998
2.3391-2.57440.16911454.51290.1564306899
2.5744-2.94680.21251434.41360.1646309799
2.9468-3.7120.16881494.5790.14883105100
3.712-34.98750.16521494.6030.1356308898
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)
11.2941-0.6107-0.40663.86263.90585.15060.0410.0045-0.24190.2056-0.00580.02010.4834-0.0326-0.06760.170.0018-0.02550.11770.00280.1501-6.4559-21.207565.5857
22.6322-0.45071.84532.1396-0.87043.5751-0.1039-0.23520.00480.09870.11890.0882-0.0541-0.2511-0.01280.09050.00410.01090.1182-0.00560.0832-18.974-7.336470.5247
32.5858-1.0222-0.73673.05731.90273.14110.0156-0.0029-0.0559-0.02350.1331-0.29140.03010.322-0.1410.1128-0.00420.0070.1432-0.00310.1252-0.8944-12.851462.105
43.0078-1.0557-2.53642.63951.74115.5134-0.13750.0714-0.19790.03790.0467-0.04970.4387-0.01130.12010.1248-0.0016-0.01480.09250.00030.1186-11.3942-20.518955.5452
50.4774-0.3077-0.14770.6240.08131.23780.003-0.00250.0241-0.04140.0273-0.03880.00070.0736-0.03180.1005-0.0083-0.00670.0947-0.00010.0896-14.1728-11.488151.3855
60.9289-0.19390.42241.21520.06931.5440.0560.0581-0.1033-0.0632-0.0116-0.0343-0.01370.0101-0.03320.1011-0.0025-0.00510.1065-0.0060.0957-20.6842-8.668739.0626
72.49290.6621-0.76263.3563-1.42963.79980.05850.00650.1527-0.0945-0.0182-0.1512-0.19020.1639-0.03750.0686-0.0033-0.00080.0527-0.01270.0643-20.3709-0.266943.2166
82.75570.24950.17012.3028-0.11182.14510.08180.20510.0863-0.21860.02380.063-0.0865-0.2013-0.10510.09130.0149-0.00620.05260.00930.0612-30.7991.665741.0634
91.22430.2946-0.03421.733-0.4411.1042-0.06010.02490.1397-0.13830.0164-0.057-0.10570.02990.04110.1186-0.00740.00090.0670.00310.0796-25.140110.070544.4827
100.9852-0.0026-0.70294.1596-0.83240.97670.0053-0.07130.10440.2647-0.0054-0.0516-0.1235-0.01020.01150.1636-0.0015-0.01840.11630.00330.1255-28.797516.684648.0345
110.219-0.53010.3891.9948-0.09881.6925-0.2591-0.38070.55380.19170.1440.0555-0.14830.1308-0.01340.17410.0365-0.04480.2242-0.07490.2496-21.55969.962663.3259
124.2840.64020.78611.4371-0.1620.2031-0.20510.45880.47360.07510.1454-0.0271-0.062-0.1142-0.08810.16840.0379-0.05770.4726-0.21230.5438-28.544514.049263.7751
133.6011.33950.85795.8232-0.48810.9486-0.2810.16650.4952-0.50580.2057-0.75530.4340.4880.12730.25340.08240.04150.3130.02850.2749-10.1425.562860.8196
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 118 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 119 through 143 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 144 through 162 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 163 through 178 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 179 through 206 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 207 through 229 )A0
11X-RAY DIFFRACTION11chain 'B' and (resid 1 through 12 )B0
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 6 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 7 through 12 )C0

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