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

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Basic information

Entry
Database: PDB / ID: 4enm
TitleCrystal structure of S. pombe Atl1 in complex with damaged DNA containing O6-benzylguanine
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*(BZG)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 / transcription-coupled nucleotide-excision repair / catalytic activity / 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: 2.8402 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 1.2Sep 13, 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 / 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_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*(BZG)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)21,6963
Polymers21,6963
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-13 kcal/mol
Surface area9610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.900, 59.900, 237.051
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*(BZG)P*CP*TP*AP*GP*TP*A)-3')


Mass: 4081.733 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)

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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: 2.96 Å3/Da / Density % sol: 58.47 %
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: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 25, 2008
RadiationMonochromator: Curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.84→50 Å / Num. all: 6178 / Num. obs: 6178 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.84→2.94 Å / % possible all: 61.1

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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
Starting model: PDB ENTRY 3GVA

3gva


Resolution: 2.8402→39.033 Å / SU ML: 0.37 / σ(F): 0.11 / Phase error: 26.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2526 590 9.97 %RANDOM
Rwork0.1732 ---
obs0.1812 5915 89.99 %-
all-5915 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 67.163 Å2 / ksol: 0.314 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-15.005 Å2-0 Å2-0 Å2
2--15.005 Å2-0 Å2
3----30.0101 Å2
Refinement stepCycle: LAST / Resolution: 2.8402→39.033 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms890 534 0 0 1424
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081512
X-RAY DIFFRACTIONf_angle_d1.2752151
X-RAY DIFFRACTIONf_dihedral_angle_d25.572616
X-RAY DIFFRACTIONf_chiral_restr0.065226
X-RAY DIFFRACTIONf_plane_restr0.004187
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8402-3.12590.37521020.2978929X-RAY DIFFRACTION66
3.1259-3.57790.24111530.19281365X-RAY DIFFRACTION96
3.5779-4.50670.23481600.15831464X-RAY DIFFRACTION99
4.5067-39.0370.24341750.15931567X-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)
11.1182-1.09830.66182.0804-1.90621.8666-1.3337-1.699-0.72920.7297-0.083-0.4809-0.4833-0.9554-0.09080.4816-0.12580.33320.90070.00720.878532.7237-23.259719.6716
20.0474-0.21790.01290.9452-0.0480.3273-1.12880.69821.12240.9969-0.7899-0.9156-0.0067-1.890.02180.70930.1351-0.05280.8646-0.22780.668330.1168-19.171213.9637
30.17210.09-0.0050.7085-0.26860.09740.7937-1.26283.05281.253-0.9719-1.3877-2.8951-0.1264-0.0320.71460.02890.23150.87370.08320.880432.2269-13.09155.9153
40.65790.2183-0.30930.0703-0.11170.0403-0.1762-0.53422.35660.26951.2354-0.5179-2.3304-0.47240.01620.95910.36690.08740.84040.13121.047930.5143-14.8439-2.8125
51.753-1.05783.47190.7927-1.31967.9810.2744-0.55540.7418-1.3521-0.8397-0.69163.82710.60190.05920.41960.01210.20390.7021-0.17070.989835.7698-23.22594.9532
60.21840.4165-0.02912.36851.16692.16550.57230.41391.0964-1.8493-1.035-3.2490.20433.2761-0.02980.26610.15050.02820.59710.08230.830436.8858-27.602511.5308
70.16670.00260.2950.1711-0.09690.469-0.4458-2.44980.7331-0.47590.44780.03591.6588-0.50290.00280.5042-0.03370.23460.89380.0680.700127.9272-28.73569.3148
80.71430.16070.08121.11171.35562.2850.0533-1.59710.48470.53970.45031.2310.9346-1.9967-0.02220.3829-0.03520.33781.16910.0591.079320.207-20.558310.9369
9-0.0032-0.14320.0361.3935-0.11710.0065-0.45590.05372.61850.58280.39571.65322.3166-0.9221-0.01721.19220.30220.27381.4971-0.23490.861321.213-11.6598.4439
100.2878-0.00050.04350.43840.27670.14140.3086-0.73650.72-1.2596-0.9685-1.0581-0.98940.0705-0.00360.58690.15550.03440.6332-0.07540.776925.0324-17.48831.038
110.16630.0442-0.13170.0135-0.04580.11010.0044-0.4569-1.89991.27680.12720.66261.9716-2.4082-0.00110.924-0.38890.18631.0987-0.04530.931227.7688-27.3898-5.1953
120.0107-0.07330.0393-0.0185-0.03510.2113-1.71762.5127-3.5594-2.68280.5421.28761.988-0.42880.00740.73580.05020.0251.8097-0.1051.176816.8673-28.29261.3971
130.3085-0.10290.26360.2177-0.02950.2468-0.2171-2.86370.3961-0.1643-0.6055-0.98950.0123-0.52760.02890.47050.2173-0.19181.572-0.350.886217.0891-20.2343-3.1971
140.13020.26060.18030.7284-0.00740.2473-1.7691-0.78950.2658-1.47210.74482.828-0.6279-0.75770.00890.99890.34280.03731.56580.11741.356120.4322-12.9598-5.4993
150.32580.07620.11590.02840.0160.0236-0.24491.11160.3439-3.9364-0.4796-1.6346-0.4667-0.49990.02871.3855-0.4561-0.12021.8061-0.00660.866923.5729-19.6425-13.1572
160.90571.0170.25781.18450.15670.1034-0.476-0.1297-2.3767-0.6476-0.71362.2951-0.2464-1.96770.03040.73260.06660.22721.7639-0.47851.397921.2125-28.3011-11.7942
170.0163-0.0445-0.03990.13050.23870.5319-0.5081-0.0078-0.147-1.96560.0426-0.48380.4121-0.2167-0.02681.2989-0.16310.26751.44220.22720.698632.6489-20.3521-10.8029
180.6948-0.1748-0.3982-0.03270.10220.15892.21320.67830.76390.7536-0.3797-0.5230.34230.3807-0.0020.952-0.12480.23610.96220.14462.127236.531-16.1756-3.2393
190.19470.58740.18661.29460.24920.0327-3.17261.2493-2.9442-2.74942.0767-0.12842.7693-1.11780.00162.061-0.10860.47971.35750.12341.167222.8433-45.259817.8018
201.5140.39511.51982.7354-1.70343.0680.3593-0.2290.4679-0.29350.05710.22821.4154-1.57320.00160.671-0.34840.07491.1441-0.01640.820623.9601-32.1915.3387
210.3115-0.27940.37330.2292-0.21080.17240.66620.23360.1552-0.12920.3498-2.33492.2228-0.66640.00471.31850.13980.30081.1724-0.2991.21336.8309-40.6053-5.7709
222.60771.56760.0551.57260.75860.67240.82811.9334-1.04970.28090.75470.64531.9015-2.7940.00791.15770.12310.26271.3786-0.14091.118329.0588-41.2727-7.3715
233.55342.7552.03582.79580.35492.307-0.2734-0.30980.0602-0.23880.74660.42212.6294-1.32790.00051.0685-0.19080.34731.08840.1831.029726.6123-36.62814.4888
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:6)
2X-RAY DIFFRACTION2(chain A and resid 7:11)
3X-RAY DIFFRACTION3(chain A and resid 12:18)
4X-RAY DIFFRACTION4(chain A and resid 19:24)
5X-RAY DIFFRACTION5(chain A and resid 25:31)
6X-RAY DIFFRACTION6(chain A and resid 32:37)
7X-RAY DIFFRACTION7(chain A and resid 38:43)
8X-RAY DIFFRACTION8(chain A and resid 44:50)
9X-RAY DIFFRACTION9(chain A and resid 51:55)
10X-RAY DIFFRACTION10(chain A and resid 56:60)
11X-RAY DIFFRACTION11(chain A and resid 61:66)
12X-RAY DIFFRACTION12(chain A and resid 67:74)
13X-RAY DIFFRACTION13(chain A and resid 75:79)
14X-RAY DIFFRACTION14(chain A and resid 80:85)
15X-RAY DIFFRACTION15(chain A and resid 86:91)
16X-RAY DIFFRACTION16(chain A and resid 92:98)
17X-RAY DIFFRACTION17(chain A and resid 99:103)
18X-RAY DIFFRACTION18(chain A and resid 104:108)
19X-RAY DIFFRACTION19(chain B and resid 1:4)
20X-RAY DIFFRACTION20(chain B and resid 5:9)
21X-RAY DIFFRACTION21(chain B and resid 10:13)
22X-RAY DIFFRACTION22(chain C and resid 14:19)
23X-RAY DIFFRACTION23(chain C and resid 20:26)

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