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- PDB-4ykl: Hnt3 in complex with DNA and guanosine -

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Basic information

Entry
Database: PDB / ID: 4ykl
TitleHnt3 in complex with DNA and guanosine
Components
  • Aprataxin-like protein
  • DNA (5'-D(*GP*AP*AP*TP*CP*AP*TP*AP*AP*C)-3')
KeywordsHydrolase/DNA / GMP / nucleotidyl transferase / HYDROLASE / 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
GUANOSINE / DNA / Aprataxin-like protein
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsJacewicz, A. / Chauleau, M. / Shuman, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM46330 United States
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: DNA3'pp5'G de-capping activity of aprataxin: effect of cap nucleoside analogs and structural basis for guanosine recognition.
Authors: Chauleau, M. / Jacewicz, A. / Shuman, S.
History
DepositionMar 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: Database references
Revision 1.2Jul 22, 2015Group: Database references
Revision 1.3Jul 27, 2016Group: Data collection
Revision 1.4Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)27,05210
Polymers26,2642
Non-polymers7888
Water95553
1
B: Aprataxin-like protein
A: DNA (5'-D(*GP*AP*AP*TP*CP*AP*TP*AP*AP*C)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)54,10320
Polymers52,5274
Non-polymers1,57616
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_556-x,-x+y,-z+11
Buried area6740 Å2
ΔGint-75 kcal/mol
Surface area21610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.083, 119.083, 36.564
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

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Protein / DNA chain , 2 types, 2 molecules BA

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


Mass: 23226.652 Da / Num. of mol.: 1 / Fragment: UNP residues 33-232
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: hnt3, SPCC18.09c / Plasmid: pet28b-His10-Smt3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O74859, Hydrolases
#2: DNA chain DNA (5'-D(*GP*AP*AP*TP*CP*AP*TP*AP*AP*C)-3')


Mass: 3037.031 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemical synthesis / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 61 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-GMP / GUANOSINE


Mass: 283.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O5
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 3.26 Å3/Da / Density % sol: 62.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 25% (w/v) PEG-3350, 0.15 M Mg-Acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.77 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.77 Å / Relative weight: 1
ReflectionResolution: 2.25→59.54 Å / Num. obs: 14369 / % possible obs: 100 % / Redundancy: 11.2 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 20.7
Reflection shellResolution: 2.25→2.32 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.722 / Mean I/σ(I) obs: 3.6 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XBA

4xba


Resolution: 2.25→59.54 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2402 866 6.03 %Random selection
Rwork0.18 ---
obs0.1836 14364 99.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.8 Å2
Refinement stepCycle: LAST / Resolution: 2.25→59.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1593 202 47 53 1895
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081907
X-RAY DIFFRACTIONf_angle_d1.1882620
X-RAY DIFFRACTIONf_dihedral_angle_d17.471717
X-RAY DIFFRACTIONf_chiral_restr0.044289
X-RAY DIFFRACTIONf_plane_restr0.006291
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2501-2.39110.27761570.21272203X-RAY DIFFRACTION100
2.3911-2.57570.26241340.21312239X-RAY DIFFRACTION100
2.5757-2.83490.25951360.20652253X-RAY DIFFRACTION100
2.8349-3.24510.26231390.19342224X-RAY DIFFRACTION100
3.2451-4.08840.24531250.16712282X-RAY DIFFRACTION100
4.0884-59.56230.21751750.16532297X-RAY DIFFRACTION100
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)
10.19320.0896-0.04770.0455-0.03850.0452-0.1485-0.39480.10290.4580.40750.5016-0.5458-0.28280.00030.50980.00220.05310.5001-0.03540.4986-24.585283.678232.5301
20.7508-0.3538-0.25130.8964-0.30890.86820.0977-0.25680.14370.1328-0.0320.0291-0.1444-0.1007-0.00010.3056-0.0447-0.00390.4451-0.00770.2721-19.425673.516228.5211
31.5102-0.03540.25982.25030.03580.10690.0264-0.14321.0452-0.254-0.0427-0.2198-0.70390.31280.16310.4091-0.1788-0.02650.3274-0.07160.4206-13.500690.085423.8774
40.4332-0.35560.11570.85250.41851.1491-0.02230.0325-0.0378-0.0770.0676-0.21250.27030.27660.01350.27220.02670.01750.46280.03160.3569-11.036471.888120.5309
50.846-0.89110.25711.0797-0.23921.1341-0.11990.5095-0.3042-0.1676-0.1196-0.0640.6860.40760.00350.43740.0340.05330.3913-0.01860.44-16.800661.27512.5791
60.38790.41440.30411.0559-0.1170.3866-0.1175-0.1060.0118-0.16160.06650.0801-0.0302-0.0180.00420.2543-0.04240.00580.3257-0.02420.2939-23.61879.870515.0257
70.0047-0.0219-0.02630.04260.11520.3248-0.18470.02080.33580.1315-0.30410.2034-0.3077-0.89350.00240.53320.1064-0.10330.370.05930.6617-27.614990.41029.1605
82.21910.0250.21550.997-0.25490.49280.10080.5466-0.0557-0.5701-0.12170.17650.05650.0362-0.16010.4047-0.0244-0.03120.3801-0.02350.3012-31.664669.47934.9807
91.10280.1115-0.36020.151-0.480.57480.28-0.56880.557-0.28750.25820.4736-0.62860.12150.15650.44910.0109-0.03960.26720.09780.7233-48.033581.54618.5756
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 33 through 43 )
2X-RAY DIFFRACTION2chain 'B' and (resid 44 through 76 )
3X-RAY DIFFRACTION3chain 'B' and (resid 77 through 93 )
4X-RAY DIFFRACTION4chain 'B' and (resid 94 through 119 )
5X-RAY DIFFRACTION5chain 'B' and (resid 120 through 132 )
6X-RAY DIFFRACTION6chain 'B' and (resid 133 through 183 )
7X-RAY DIFFRACTION7chain 'B' and (resid 184 through 195 )
8X-RAY DIFFRACTION8chain 'B' and (resid 196 through 230 )
9X-RAY DIFFRACTION9chain 'A' and (resid 1 through 10 )

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