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- PDB-3szq: Structure of an S. pombe APTX/DNA/AMP/Zn complex -

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Basic information

Entry
Database: PDB / ID: 3szq
TitleStructure of an S. pombe APTX/DNA/AMP/Zn complex
Components
  • 5'-D(*CP*CP*CP*TP*G)-3'
  • 5'-D(*TP*AP*TP*CP*GP*GP*AP*AP*TP*CP*AP*GP*GP*G)-3'
  • Aprataxin-like protein
KeywordsHYDROLASE/DNA / histidine triad (HIT) / C2HE zinc finger / DNA repair / HYDROLASE-DNA complex
Function / homology
Function and homology information


guanosine binding / adenosine-5'-diphospho-5'-[DNA] diphosphatase / DNA-3'-diphospho-5'-guanosine diphosphatase / DNA-3'-diphospho-5'-guanosine diphosphatase / DNA 5'-adenosine monophosphate hydrolase activity / GMP binding / single-strand break-containing DNA binding / single strand break repair / mismatched DNA binding / mismatch repair ...guanosine binding / adenosine-5'-diphospho-5'-[DNA] diphosphatase / DNA-3'-diphospho-5'-guanosine diphosphatase / DNA-3'-diphospho-5'-guanosine diphosphatase / DNA 5'-adenosine monophosphate hydrolase activity / GMP binding / single-strand break-containing DNA binding / single strand break repair / mismatched DNA binding / mismatch repair / double-stranded RNA binding / single-stranded DNA binding / double-stranded DNA binding / zinc ion binding / nucleus / cytosol
Similarity search - Function
Aprataxin, C2HE/C2H2/C2HC zinc finger / C2HE / C2H2 / C2HC zinc-binding finger / HIT domain / HIT-like domain / HIT-like / HIT family, subunit A / HIT-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / BETA-MERCAPTOETHANOL / DNA / DNA (> 10) / Aprataxin-like protein
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.353 Å
AuthorsTumbale, P. / Krahn, J. / Williams, R.S.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Structure of an aprataxin-DNA complex with insights into AOA1 neurodegenerative disease.
Authors: Tumbale, P. / Appel, C.D. / Kraehenbuehl, R. / Robertson, P.D. / Williams, J.S. / Krahn, J. / Ahel, I. / Williams, R.S.
History
DepositionJul 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2011Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aprataxin-like protein
B: 5'-D(*CP*CP*CP*TP*G)-3'
C: 5'-D(*TP*AP*TP*CP*GP*GP*AP*AP*TP*CP*AP*GP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2677
Polymers29,6983
Non-polymers5694
Water3,801211
1
A: Aprataxin-like protein
B: 5'-D(*CP*CP*CP*TP*G)-3'
C: 5'-D(*TP*AP*TP*CP*GP*GP*AP*AP*TP*CP*AP*GP*GP*G)-3'
hetero molecules

A: Aprataxin-like protein
B: 5'-D(*CP*CP*CP*TP*G)-3'
C: 5'-D(*TP*AP*TP*CP*GP*GP*AP*AP*TP*CP*AP*GP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,53414
Polymers59,3976
Non-polymers1,1388
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Unit cell
Length a, b, c (Å)157.050, 157.050, 157.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432
Components on special symmetry positions
IDModelComponents
11A-8-

HOH

21A-261-

HOH

31A-283-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Aprataxin-like protein / Hit family protein 3


Mass: 23897.436 Da / Num. of mol.: 1
Fragment: APTX HIT-ZNF catalytic domain (UNP residues 31-232)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: ATCC 38366 / 972 / Gene: hnt3, SPCC18.09c / Production host: Escherichia coli (E. coli) / References: UniProt: O74859, Hydrolases

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain 5'-D(*CP*CP*CP*TP*G)-3'


Mass: 1455.987 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5'-D(*TP*AP*TP*CP*GP*GP*AP*AP*TP*CP*AP*GP*GP*G)-3'


Mass: 4344.840 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 4 types, 215 molecules

#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.72 Å3/Da / Density % sol: 54.73 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 10
Details: 0.2 M sodium/potassium tartrate, 20% w/v PEG3350, pH 10.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.283 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 28, 2010
RadiationMonochromator: Si(111) Rosenbaum-Rock double-crystal monochromator: LN2-cooled, sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.283 Å / Relative weight: 1
ReflectionResolution: 2.35→49.663 Å / Num. all: 14068 / Num. obs: 14067 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 4.7 / Redundancy: 7.7 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 20.9
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.462 / Mean I/σ(I) obs: 4.7 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.353→24.832 Å / SU ML: 0.28 / σ(F): 1.28 / Phase error: 20.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.211 1250 4.81 %RANDOM
Rwork0.165 ---
all0.1673 14068 --
obs0.165 14067 99.96 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.41 Å2 / ksol: 0.336 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.353→24.832 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1615 264 32 211 2122
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092046
X-RAY DIFFRACTIONf_angle_d1.0622829
X-RAY DIFFRACTIONf_dihedral_angle_d17.047766
X-RAY DIFFRACTIONf_chiral_restr0.065313
X-RAY DIFFRACTIONf_plane_restr0.004308
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3532-2.44740.26981360.20762780X-RAY DIFFRACTION100
2.4474-2.55860.27871420.19332731X-RAY DIFFRACTION100
2.5586-2.69340.23611350.18572726X-RAY DIFFRACTION100
2.6934-2.86190.30041290.17742768X-RAY DIFFRACTION100
2.8619-3.08250.21031400.17272755X-RAY DIFFRACTION100
3.0825-3.3920.23651190.15692757X-RAY DIFFRACTION100
3.392-3.88120.18691540.15512732X-RAY DIFFRACTION100
3.8812-4.88380.1581600.13082713X-RAY DIFFRACTION100
4.8838-24.83320.20731350.17732780X-RAY DIFFRACTION100

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