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- PDB-5lw6: Crystal structure of a Se-Met substituted Dictyostelium discoideu... -

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Basic information

Entry
Database: PDB / ID: 5lw6
TitleCrystal structure of a Se-Met substituted Dictyostelium discoideum ADP-ribose binding macrodomain (residues 342-563) of DDB_G0293866
ComponentsDDB_G0293866
KeywordsADP-RIBOSE BINDING PROTEIN / Macrodomain
Function / homology
Function and homology information


response to cisplatin / poly-ADP-D-ribose binding / DNA damage sensor activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / 3'-5' exonuclease activity / double-strand break repair / site of double-strand break / nucleus
Similarity search - Function
Aprataxin and PNK-like factor, PBZ domain / Aprataxin and PNK-like factor / PBZ domain / SMAD/FHA domain superfamily / Macro domain-like
Similarity search - Domain/homology
Aprataxin and PNK-like factor PBZ domain-containing protein
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsLeys, D. / Barkauskaite, E. / Pinero, B.B. / Ahel, I.
CitationJournal: J.Cell.Sci. / Year: 2016
Title: The role of ADP-ribosylation in regulating DNA interstrand crosslink repair.
Authors: Gunn, A.R. / Banos-Pinero, B. / Paschke, P. / Sanchez-Pulido, L. / Ariza, A. / Day, J. / Emrich, M. / Leys, D. / Ponting, C.P. / Ahel, I. / Lakin, N.D.
History
DepositionSep 15, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2016Group: Database references
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DDB_G0293866


Theoretical massNumber of molelcules
Total (without water)29,4741
Polymers29,4741
Non-polymers00
Water1,856103
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.590, 71.220, 81.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DDB_G0293866


Mass: 29474.408 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: DDB0192167 / Production host: Escherichia coli (E. coli) / References: UniProt: Q54B72
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.98 Å3/Da / Density % sol: 37.99 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: Crystallization trials were performed with proteins at 25 mg/ml in buffer containing 150 mM NaCl, 1 mM DTT and 25 mM Tris-HCl (pH 7.5), at 20 C with commercial screens using the sitting-drop ...Details: Crystallization trials were performed with proteins at 25 mg/ml in buffer containing 150 mM NaCl, 1 mM DTT and 25 mM Tris-HCl (pH 7.5), at 20 C with commercial screens using the sitting-drop vapour-diffusion method. Crystallization drops were set up with the aid of a Mosquito Crystal robot (TTP Labtech) using 200 nl of protein solution plus 200 nl of reservoir solution in MRC two-well crystallization microplates (Swissci) equilibrated against 75 microl of reservoir solution. Co-crystallisation trials were set up by adding 2 mM ADPr to the protein for at least 1 hour prior to setting up crystallisation drops. Crystals of the macrodomain proteins grew in 0.2 M Lithium sulphate, 0.1 M phosphate/citrate and 20% (w/v) PEG1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.8→25.19 Å / Num. obs: 22050 / % possible obs: 99.9 % / Redundancy: 25.8 % / Rsym value: 0.078 / Net I/σ(I): 17.3
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 25.4 % / Mean I/σ(I) obs: 5.3 / Rsym value: 0.943 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XDSdata scaling
MLPHAREphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→25.19 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.319 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.119 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21433 1131 5.1 %RANDOM
Rwork0.16982 ---
obs0.17205 20867 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.915 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0 Å2
2--0.02 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.8→25.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1786 0 0 103 1889
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191836
X-RAY DIFFRACTIONr_bond_other_d0.0020.021785
X-RAY DIFFRACTIONr_angle_refined_deg1.8981.9732475
X-RAY DIFFRACTIONr_angle_other_deg0.90834135
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.145226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.83525.35784
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.13815341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.446155
X-RAY DIFFRACTIONr_chiral_restr0.1180.2271
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022052
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02415
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.803→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 77 -
Rwork0.166 1495 -
obs--100 %

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