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- PDB-4hdu: Crystal structure of S. pombe ATL1 in complex with damaged DNA co... -

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Basic information

Entry
Database: PDB / ID: 4hdu
TitleCrystal structure of S. pombe ATL1 in complex with damaged DNA containing 2-aminopurine
Components
  • 5'-D(*CP*TP*AP*CP*TP*AP*GP*CP*CP*AP*TP*GP*G)-3'
  • 5'-D(*GP*CP*CP*AP*TP*GP*(2PR)P*CP*TP*AP*GP*TP*A)-3'
  • Alkyltransferase-like protein 1
KeywordsDNA BINDING PROTEIN/DNA / alkyltransferase / DNA repair / nucleotide excision repair / NER / base repair / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.848 Å
AuthorsTubbs, J.L. / Tainer, J.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Alkyltransferase-like protein (Atl1) distinguishes alkylated guanines for DNA repair using cation-{pi} interactions.
Authors: Wilkinson, O.J. / Latypov, V. / Tubbs, J.L. / Millington, C.L. / Morita, R. / Blackburn, H. / Marriott, A. / McGown, G. / Thorncroft, M. / Watson, A.J. / Connolly, B.A. / Grasby, J.A. / ...Authors: Wilkinson, O.J. / Latypov, V. / Tubbs, J.L. / Millington, C.L. / Morita, R. / Blackburn, H. / Marriott, A. / McGown, G. / Thorncroft, M. / Watson, A.J. / Connolly, B.A. / Grasby, J.A. / Masui, R. / Hunter, C.A. / Tainer, J.A. / Margison, G.P. / Williams, D.M.
History
DepositionOct 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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_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_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: 5'-D(*GP*CP*CP*AP*TP*GP*(2PR)P*CP*TP*AP*GP*TP*A)-3'
C: 5'-D(*CP*TP*AP*CP*TP*AP*GP*CP*CP*AP*TP*GP*G)-3'


Theoretical massNumber of molelcules
Total (without water)21,5903
Polymers21,5903
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-10 kcal/mol
Surface area9490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.978, 59.978, 235.488
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 / ATL1


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


Mass: 3975.611 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 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

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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: 2.83 Å3/Da / Density % sol: 56.56 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 20% mPEG2000, 0.5 M sodium formate, 200 mM 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: May 21, 2011
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.848→50 Å / Num. all: 6482 / Num. obs: 6482 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 19.9 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 83.6
Reflection shellResolution: 2.848→2.95 Å / Redundancy: 20.9 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 12.2 / % possible all: 100

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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: 2.848→34.89 Å / SU ML: 0.4 / σ(F): 0.21 / Phase error: 25.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2669 640 10.08 %RANDOM
Rwork0.2134 ---
obs0.2191 6352 97.9 %-
all-6352 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.577 Å2 / ksol: 0.331 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.4043 Å20 Å2-0 Å2
2--8.4043 Å2-0 Å2
3----16.8087 Å2
Refinement stepCycle: LAST / Resolution: 2.848→34.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms890 526 0 0 1416
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061541
X-RAY DIFFRACTIONf_angle_d0.782153
X-RAY DIFFRACTIONf_dihedral_angle_d22.584616
X-RAY DIFFRACTIONf_chiral_restr0.039227
X-RAY DIFFRACTIONf_plane_restr0.002188
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.848-3.06790.33311160.28091041X-RAY DIFFRACTION93
3.0679-3.37640.31851240.21781106X-RAY DIFFRACTION98
3.3764-3.86450.2681270.2281124X-RAY DIFFRACTION99
3.8645-4.86670.26611300.19361164X-RAY DIFFRACTION100
4.8667-34.8930.23351430.20121277X-RAY DIFFRACTION99

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