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

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Basic information

Entry
Database: PDB / ID: 4enk
TitleCrystal structure of S. pombe Atl1 in complex with damaged DNA containing O6-propylguanine
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*(6PO)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: 3.0445 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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*(6PO)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)21,6483
Polymers21,6483
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-10 kcal/mol
Surface area9710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.501, 59.501, 236.917
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*(6PO)P*CP*TP*AP*GP*TP*A)-3')


Mass: 4033.689 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 / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.93 Å3/Da / Density % sol: 57.99 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 25% mPEG 2000, 5% sodium formate, 0.2M imidazole-malate, pH 5.8, 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: Feb 19, 2009
RadiationMonochromator: ML crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 3.0445→50 Å / Num. all: 5247 / Num. obs: 5247 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.0445→3.16 Å / % possible all: 82.3

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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: 3.0445→34.879 Å / SU ML: 0.28 / σ(F): 0.17 / Phase error: 38.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2952 484 10.09 %RANDOM
Rwork0.2499 ---
all0.2544 4797 --
obs0.2544 4797 90.19 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.536 Å2 / ksol: 0.239 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-24.9246 Å2-0 Å2-0 Å2
2--24.9246 Å2-0 Å2
3----49.8492 Å2
Refinement stepCycle: LAST / Resolution: 3.0445→34.879 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms890 530 0 1 1421
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011516
X-RAY DIFFRACTIONf_angle_d1.6512158
X-RAY DIFFRACTIONf_dihedral_angle_d27.221619
X-RAY DIFFRACTIONf_chiral_restr0.088227
X-RAY DIFFRACTIONf_plane_restr0.008188
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0445-3.48470.43251310.31831163X-RAY DIFFRACTION76
3.4847-4.3890.33471670.26051467X-RAY DIFFRACTION95
4.389-34.88120.26231860.23251683X-RAY DIFFRACTION99

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