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- PDB-3spd: Crystal structure of aprataxin ortholog Hnt3 in complex with DNA -

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Basic information

Entry
Database: PDB / ID: 3spd
TitleCrystal structure of aprataxin ortholog Hnt3 in complex with DNA
Components
  • Aprataxin-like protein
  • DNA (5'-D(*GP*TP*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*AP*TP*GP*AP*G)-3')
  • DNA (5'-D(*TP*AP*TP*TP*CP*CP*GP*AP*TP*AP*GP*TP*GP*AP*C)-3')
KeywordsHYDROLASE/DNA / HIT domain / Zinc Finger / DNA deadenylase / DNA Binding / HYDROLASE-DNA complex
Function / homology
Function and homology information


guanosine binding / adenosine-5'-diphospho-5'-[DNA] diphosphatase / DNA-3'-diphospho-5'-guanosine diphosphatase / DNA 5'-adenosine monophosphate hydrolase activity / DNA-3'-diphospho-5'-guanosine diphosphatase activity / single-strand break-containing DNA binding / mismatched DNA binding / single strand break repair / GMP binding / mismatch repair ...guanosine binding / adenosine-5'-diphospho-5'-[DNA] diphosphatase / DNA-3'-diphospho-5'-guanosine diphosphatase / DNA 5'-adenosine monophosphate hydrolase activity / DNA-3'-diphospho-5'-guanosine diphosphatase activity / single-strand break-containing DNA binding / mismatched DNA binding / single strand break repair / GMP binding / mismatch repair / single-stranded DNA binding / double-stranded RNA 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
DNA / DNA (> 10) / Aprataxin-like protein
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.912 Å
AuthorsGong, Y. / Zhu, D. / Ding, J. / Dou, C. / Ren, X. / Jiang, T. / Wang, D.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Crystal structures of aprataxin ortholog Hnt3 reveal the mechanism for reversal of 5'-adenylated DNA
Authors: Gong, Y. / Zhu, D. / Ding, J. / Dou, C. / Ren, X. / Gu, L. / Jiang, T. / Wang, D.
History
DepositionJul 1, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Nov 1, 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 / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_asym_id / _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_asym_id / _struct_conn.ptnr2_label_asym_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: Aprataxin-like protein
C: Aprataxin-like protein
D: Aprataxin-like protein
E: DNA (5'-D(*TP*AP*TP*TP*CP*CP*GP*AP*TP*AP*GP*TP*GP*AP*C)-3')
F: DNA (5'-D(*GP*TP*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*AP*TP*GP*AP*G)-3')
G: DNA (5'-D(*TP*AP*TP*TP*CP*CP*GP*AP*TP*AP*GP*TP*GP*AP*C)-3')
H: DNA (5'-D(*GP*TP*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*AP*TP*GP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,90228
Polymers114,1038
Non-polymers1,79920
Water19,9071105
1
A: Aprataxin-like protein
B: Aprataxin-like protein
E: DNA (5'-D(*TP*AP*TP*TP*CP*CP*GP*AP*TP*AP*GP*TP*GP*AP*C)-3')
F: DNA (5'-D(*GP*TP*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*AP*TP*GP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,95114
Polymers57,0524
Non-polymers89910
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-127 kcal/mol
Surface area23620 Å2
MethodPISA
2
C: Aprataxin-like protein
D: Aprataxin-like protein
G: DNA (5'-D(*TP*AP*TP*TP*CP*CP*GP*AP*TP*AP*GP*TP*GP*AP*C)-3')
H: DNA (5'-D(*GP*TP*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*AP*TP*GP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,95114
Polymers57,0524
Non-polymers89910
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-128 kcal/mol
Surface area23640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)220.409, 220.409, 135.031
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11D-235-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Aprataxin-like protein / Hnt3 protein / Hit family protein 3


Mass: 23608.061 Da / Num. of mol.: 4 / Fragment: UNP residues 33-232 / Mutation: C130A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: ATCC 38366 / 972 / Gene: hnt3, SPCC18.09c / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: O74859

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DNA chain , 2 types, 4 molecules EGFH

#2: DNA chain DNA (5'-D(*TP*AP*TP*TP*CP*CP*GP*AP*TP*AP*GP*TP*GP*AP*C)-3')


Mass: 4583.996 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: DNA oligonucleotides were synthesized from Shanghai Sangon Biotechnology Company (Shanghai, China).
#3: DNA chain DNA (5'-D(*GP*TP*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*AP*TP*GP*AP*G)-3')


Mass: 5251.423 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: DNA oligonucleotides were synthesized from Shanghai Sangon Biotechnology Company (Shanghai, China)

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Non-polymers , 3 types, 1125 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1105 / 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: 2.77 Å3/Da / Density % sol: 55.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.6M Ammonium Sulfate, 0.1M HEPES, pH7.5 , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 2, 2010
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.91→50 Å / Num. all: 96371 / Num. obs: 96371 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.8 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 32.6
Reflection shellResolution: 1.91→1.98 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 4.1 / Num. unique all: 9158 / Rsym value: 0.481 / % possible all: 95

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SP4

3sp4


Resolution: 1.912→23.496 Å / Occupancy max: 1 / Occupancy min: 0.39 / SU ML: 1.69 / σ(F): 0.12 / σ(I): 0.12 / Phase error: 20.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2115 4616 5.04 %RANDOM
Rwork0.1746 ---
obs0.1765 91549 94.91 %-
all-91580 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.38 Å2 / ksol: 0.375 e/Å3
Displacement parametersBiso max: 89.45 Å2 / Biso mean: 27.2893 Å2 / Biso min: 11.07 Å2
Baniso -1Baniso -2Baniso -3
1--0.0371 Å2-0 Å20 Å2
2---0.0371 Å2-0 Å2
3---0.0742 Å2
Refinement stepCycle: LAST / Resolution: 1.912→23.496 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6516 1138 84 1105 8843
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078042
X-RAY DIFFRACTIONf_angle_d1.08511140
X-RAY DIFFRACTIONf_dihedral_angle_d19.5592998
X-RAY DIFFRACTIONf_chiral_restr0.0671227
X-RAY DIFFRACTIONf_plane_restr0.0051210
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9118-1.93350.23871230.1934253382
1.9335-1.95620.22281500.1752271688
1.9562-1.98010.24141380.182264989
1.9801-2.00510.24311430.1792279591
2.0051-2.03150.25731490.1761270490
2.0315-2.05930.21821540.167281892
2.0593-2.08870.20251350.159280692
2.0887-2.11990.2061480.1685285293
2.1199-2.1530.22041470.1664282394
2.153-2.18820.22141380.1611288395
2.1882-2.22590.20471360.1758289394
2.2259-2.26640.23051550.1727286295
2.2664-2.30990.2241580.1725288095
2.3099-2.3570.21251620.1743289095
2.357-2.40820.20661610.1699291496
2.4082-2.46420.24161460.1762290895
2.4642-2.52580.20721530.1769287296
2.5258-2.5940.20571550.192299097
2.594-2.67020.25461610.2057288396
2.6702-2.75630.25251800.2062298798
2.7563-2.85460.26831720.2031295998
2.8546-2.96870.2291750.1937293298
2.9687-3.10350.2371450.187303198
3.1035-3.26670.21591770.18298198
3.2667-3.47080.16241590.1557302798
3.4708-3.73780.18951660.153302198
3.7378-4.11210.17361470.144304699
4.1121-4.7030.16931580.1453303299
4.703-5.90970.18151540.17073114100
5.9097-23.49770.21841710.1935313299

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