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- PDB-4enj: Crystal structure of S. pombe Atl1 in complex with damaged DNA co... -

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Basic information

Entry
Database: PDB / ID: 4enj
TitleCrystal structure of S. pombe Atl1 in complex with damaged DNA containing O6-hydroxyethylguanine
Components
  • Alkyltransferase-like protein 1
  • DNA (5'-D(*CP*TP*AP*CP*TP*AP*GP*CP*CP*AP*TP*GP*G)-3')
  • DNA (5'-D(*GP*CP*CP*AP*TP*GP*(EHG)P*CP*TP*AP*GP*TP*A)-3')
KeywordsDNA BINDING PROTEIN/DNA / Alkyltransferase / DNA repair / nucleotide excision repair / NER / base repair / DNA / DNA Damage / Guanine / Alkylation / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


O6-alkylguanine-DNA binding / global genome nucleotide-excision repair / catalytic activity / transcription-coupled nucleotide-excision repair / damaged DNA binding / nucleus / cytosol
Similarity search - Function
: / Methylated-DNA-[protein]-cysteine S-methyltransferase, DNA binding / Methylated DNA-protein cysteine methyltransferase, DNA binding domain / 6-O-methylguanine DNA methyltransferase, DNA binding domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Alkyltransferase-like protein 1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.0989 Å
AuthorsTubbs, J.L. / Arvai, A.S. / Tainer, J.A.
CitationJournal: Mol.Cell / Year: 2012
Title: Atl1 Regulates Choice between Global Genome and Transcription-Coupled Repair of O(6)-Alkylguanines.
Authors: Latypov, V.F. / Tubbs, J.L. / Watson, A.J. / Marriott, A.S. / McGown, G. / Thorncroft, M. / Wilkinson, O.J. / Senthong, P. / Butt, A. / Arvai, A.S. / Millington, C.L. / Povey, A.C. / ...Authors: Latypov, V.F. / Tubbs, J.L. / Watson, A.J. / Marriott, A.S. / McGown, G. / Thorncroft, M. / Wilkinson, O.J. / Senthong, P. / Butt, A. / Arvai, A.S. / Millington, C.L. / Povey, A.C. / Williams, D.M. / Santibanez-Koref, M.F. / Tainer, J.A. / Margison, G.P.
History
DepositionApr 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_polymer_linkage / struct_conn / struct_ref_seq / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alkyltransferase-like protein 1
B: DNA (5'-D(*GP*CP*CP*AP*TP*GP*(EHG)P*CP*TP*AP*GP*TP*A)-3')
C: DNA (5'-D(*CP*TP*AP*CP*TP*AP*GP*CP*CP*AP*TP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)21,6503
Polymers21,6503
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-12 kcal/mol
Surface area10020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.774, 59.774, 232.724
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Alkyltransferase-like protein 1


Mass: 13662.412 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / ATCC 24843 / Gene: atl1, SPAC1250.04c / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UTN9
#2: DNA chain DNA (5'-D(*GP*CP*CP*AP*TP*GP*(EHG)P*CP*TP*AP*GP*TP*A)-3')


Mass: 4035.663 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*CP*TP*AP*CP*TP*AP*GP*CP*CP*AP*TP*GP*G)-3')


Mass: 3951.586 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.: 4 / 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: 2.9 Å3/Da / Density % sol: 57.62 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 15% mPEG 2000, 0.2M imidazole-malate, 30% xylose, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.1158 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 1, 2008
RadiationMonochromator: ML crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 3.0989→50 Å / Num. all: 4929 / Num. obs: 4929 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.0989→3.21 Å / % possible all: 77.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.0989→38.674 Å / SU ML: 0.43 / σ(F): 0.17 / Phase error: 30.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2828 448 9.98 %RANDOM
Rwork0.2254 ---
obs0.2311 4488 89.49 %-
all-4488 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 113.258 Å2 / ksol: 0.323 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-15.5158 Å2-0 Å2-0 Å2
2--15.5158 Å2-0 Å2
3----31.0315 Å2
Refinement stepCycle: LAST / Resolution: 3.0989→38.674 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms890 530 0 4 1424
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011507
X-RAY DIFFRACTIONf_angle_d1.5932144
X-RAY DIFFRACTIONf_dihedral_angle_d26.194615
X-RAY DIFFRACTIONf_chiral_restr0.082226
X-RAY DIFFRACTIONf_plane_restr0.007186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0989-3.5470.36591170.29061077X-RAY DIFFRACTION75
3.547-4.46780.27361530.23771389X-RAY DIFFRACTION94
4.4678-38.67690.26931780.20671574X-RAY DIFFRACTION98
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)
1-0.0143-0.34180.0280.143-0.0079-0.0615-1.150.6627-3.1330.11320.41760.4414-0.179-1.649201.658-0.05540.31471.5022-0.37321.455338.1934-20.119921.4299
20.0198-0.02290.0197-0.0211-0.08450.1178-0.0455-2.0238-2.13360.6338-1.08280.7612-0.92471.504-01.1908-0.1972-0.10761.1513-0.221.684636.8162-17.856214.8965
30.1574-0.06590.18890.0993-0.1627-0.0052-1.638-0.3635-1.81340.5166-0.5232-2.5550.34620.91901.4676-0.2110.57971.21170.25982.158737.4157-12.38958.6081
4-0.3020.1837-0.1480.058-0.07260.02331.79480.43844.0507-1.84190.2681-0.58841.2354-0.5597-02.03350.25980.68491.66420.09091.895537.9646-11.4989-3.0881
5-0.09090.10910.06780.18130.17130.09391.77091.1289-2.4814-0.2312-0.4495-1.16922.49420.240301.39080.02920.12571.5058-0.03021.459340.3501-22.89994.1242
60.18280.17060.01180.16290.65150.51711.4364-1.10142.1630.8194-1.3067-0.9349-0.88953.106-01.0272-0.09020.14161.2702-0.06241.841742.3152-24.380211.738
7-0.0521-0.0298-0.10160.2222-0.22470.2042-1.82920.06470.69150.51091.0743.19172.7394-1.85-01.0701-0.25550.19821.65920.03331.325132.333-26.60969.9747
8-0.08840.2612-0.04880.10260.229-0.0873-0.0641-3.8620.31871.6312-1.98891.1754-0.8614-1.152500.7135-0.2229-0.01941.8226-0.40291.878727.3056-19.869210.0353
90.1779-0.37190.19470.154-0.02070.16310.1091.1934-0.68550.14561.1991-0.0662-1.143-1.750101.38970.2011-0.03951.722-0.35071.768224.0864-9.97769.1312
10-0.1166-0.51690.16850.13510.0594-0.0348-1.16063.47021.02211.02350.26522.8824-1.1007-1.420501.6996-0.24-0.10191.9177-0.07821.394530.9331-14.36951.8488
11-0.1403-0.11490.01120.02210.03840.0665-1.2881-0.1628-2.28320.3629-1.41340.7546-0.7428-2.570101.76560.28420.30861.3757-0.13521.515734.8823-26.8163-3.5024
120.1524-0.09550.1425-0.13660.10660.02940.92790.61120.45881.01120.55461.7228-0.4509-0.7988-01.6843-0.55530.2641.8901-0.06421.60125.3699-27.1301-0.2649
130.29940.11440.02510.31550.48750.1986-0.08881.4080.12710.07080.40920.90551.4102-1.7149-0.00011.49360.0856-0.13711.471-0.37421.457820.8622-22.7105-1.19
14-0.3322-0.35550.23740.0499-0.0181-0.00720.796-1.99620.38770.5271.26630.9235-1.1634-2.3264-01.7534-0.0199-0.02331.9507-0.18521.358524.6935-15.4007-4.133
15-0.08350.15220.07210.0159-0.05620.0740.11020.3131-0.7464-0.20530.92223.2403-2.5745-1.42730.00012.28660.1096-0.04471.3236-0.01911.835330.175-11.8001-8.7761
16-0.0355-0.3522-0.20850.02360.0164-0.0608-0.57820.2217-1.8104-0.18641.3988-0.3644-3.5589-3.2524-02.24140.34140.02232.3393-0.21871.401429.4599-21.6918-14.0813
170.16090.38670.12530.0377-0.28820.08221.3327-2.5297-0.84990.1886-2.58711.3055-1.77984.1573-02.1896-0.16760.18882.6167-0.34161.598127.3341-27.9377-11.07
180.03110.11030.1435-0.05850.06110.1262-1.4742-0.0605-3.42930.12891.0116-0.87120.5522-0.9288-01.6396-0.48850.39622.1528-0.20411.835839.7859-20.2957-10.2191
190.1403-0.3386-0.14290.29430.0030.0296-0.4010.71621.09440.85340.8657-1.4679-1.5268-0.62850.00012.2546-0.09690.7651.9381-0.0722.246444.613-15.6577-2.3736
200.01910.1480.21090.51950.1109-0.0205-1.4071-1.7792-1.329-1.07711.1179-0.4232.8212-0.907702.0594-0.00710.41441.85350.15161.370126.4083-41.562620.0664
21-1.1036-0.42892.51732.7791-0.18321.19290.38370.60320.2195-0.2292-0.48710.58571.0632-0.871101.294-0.18940.26941.2112-0.21611.441331.4327-31.29015.421
221.03961.2173-0.79741.54140.48060.56260.1086-0.4158-0.70030.8390.82550.53250.3049-0.86901.74430.14890.17021.8445-0.29271.523637.2757-40.9633-6.8211
23-0.2221-1.1405-0.01530.3717-0.26120.03850.23180.5249-0.4612.3376-0.77491.23863.8012-0.34501.7280.01060.24531.7336-0.22091.792637.414-41.16746.401
240.0430.0275-0.33922.1508-0.02480.3334-0.1423-1.2046-0.530.3494-0.4130.82970.49670.358901.12140.06390.27981.4681-0.221.503328.1653-31.866718.6102
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:5)
2X-RAY DIFFRACTION2(chain A and resid 6:10)
3X-RAY DIFFRACTION3(chain A and resid 11:16)
4X-RAY DIFFRACTION4(chain A and resid 17:22)
5X-RAY DIFFRACTION5(chain A and resid 23:30)
6X-RAY DIFFRACTION6(chain A and resid 31:38)
7X-RAY DIFFRACTION7(chain A and resid 39:43)
8X-RAY DIFFRACTION8(chain A and resid 44:48)
9X-RAY DIFFRACTION9(chain A and resid 49:53)
10X-RAY DIFFRACTION10(chain A and resid 54:59)
11X-RAY DIFFRACTION11(chain A and resid 60:65)
12X-RAY DIFFRACTION12(chain A and resid 66:70)
13X-RAY DIFFRACTION13(chain A and resid 71:76)
14X-RAY DIFFRACTION14(chain A and resid 77:81)
15X-RAY DIFFRACTION15(chain A and resid 82:87)
16X-RAY DIFFRACTION16(chain A and resid 88:92)
17X-RAY DIFFRACTION17(chain A and resid 93:98)
18X-RAY DIFFRACTION18(chain A and resid 99:103)
19X-RAY DIFFRACTION19(chain A and resid 104:108)
20X-RAY DIFFRACTION20(chain B and resid 1:4)
21X-RAY DIFFRACTION21(chain B and resid 5:10)
22X-RAY DIFFRACTION22(chain B and resid 11:13) or (chain C and resid 14:17)
23X-RAY DIFFRACTION23(chain C and resid 18:21)
24X-RAY DIFFRACTION24(chain C and resid 22:26)

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