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- PDB-5h6n: DNA targeting ADP-ribosyltransferase Pierisin-1, autoinhibitory form -

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Basic information

Entry
Database: PDB / ID: 5h6n
TitleDNA targeting ADP-ribosyltransferase Pierisin-1, autoinhibitory form
ComponentsPierisin-1
KeywordsTRANSFERASE / DNA-targeting ADP-ribosyltransferase
Function / homology
Function and homology information


2'-deoxyguanosine DNA ADP-ribosyltransferase activity / DNA ADP-ribosylation / glycosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / nucleotidyltransferase activity / apoptotic process / DNA binding
Similarity search - Function
: / Scabin-like / Heat-Labile Enterotoxin; Chain A / Heat-Labile Enterotoxin, subunit A / Ricin-type beta-trefoil lectin domain-like / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesPieris rapae (cabbage white)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsOda, T. / Hirabayashi, H. / Shikauchi, G. / Takamura, R. / Hiraga, K. / Minami, H. / Hashimoto, H. / Yamamoto, M. / Wakabayashi, K. / Sugimura, T. ...Oda, T. / Hirabayashi, H. / Shikauchi, G. / Takamura, R. / Hiraga, K. / Minami, H. / Hashimoto, H. / Yamamoto, M. / Wakabayashi, K. / Sugimura, T. / Shimizu, T. / Sato, M.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structural basis of autoinhibition and activation of the DNA-targeting ADP-ribosyltransferase pierisin-1
Authors: Oda, T. / Hirabayashi, H. / Shikauchi, G. / Takamura, R. / Hiraga, K. / Minami, H. / Hashimoto, H. / Yamamoto, M. / Wakabayashi, K. / Shimizu, T. / Sato, M.
History
DepositionNov 14, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 8, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pierisin-1
B: Pierisin-1
C: Pierisin-1
D: Pierisin-1


Theoretical massNumber of molelcules
Total (without water)125,8254
Polymers125,8254
Non-polymers00
Water10,593588
1
A: Pierisin-1


Theoretical massNumber of molelcules
Total (without water)31,4561
Polymers31,4561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Pierisin-1


Theoretical massNumber of molelcules
Total (without water)31,4561
Polymers31,4561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Pierisin-1


Theoretical massNumber of molelcules
Total (without water)31,4561
Polymers31,4561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Pierisin-1


Theoretical massNumber of molelcules
Total (without water)31,4561
Polymers31,4561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.070, 110.500, 133.640
Angle α, β, γ (deg.)90.00, 91.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Pierisin-1


Mass: 31456.125 Da / Num. of mol.: 4 / Fragment: UNP residues 1-267 / Mutation: E165Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pieris rapae (cabbage white) / Plasmid: pGEX6p-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): codon plus RIPL
References: UniProt: H3JU00, UniProt: Q9U8Q4*PLUS, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 588 / 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: 3.06 Å3/Da / Density % sol: 59.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 22% (v/v) t-butanol and 0.1M Tris-HCl pH8

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 132451 / % possible obs: 95 % / Redundancy: 3.74 % / Net I/σ(I): 19.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CB4

2cb4


Resolution: 1.8→30.068 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.927 / SU B: 2.909 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24141 6687 5 %RANDOM
Rwork0.224 ---
obs0.22487 125934 94.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.354 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å2-0 Å2-0.64 Å2
2--0.54 Å20 Å2
3---0.18 Å2
Refinement stepCycle: 1 / Resolution: 1.8→30.068 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7885 0 0 588 8473
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0198098
X-RAY DIFFRACTIONr_bond_other_d0.0010.027530
X-RAY DIFFRACTIONr_angle_refined_deg1.1221.93311034
X-RAY DIFFRACTIONr_angle_other_deg0.88317200
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.935952
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.75623.166439
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.442151287
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1261592
X-RAY DIFFRACTIONr_chiral_restr0.0630.21158
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0219282
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022042
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_it0.9033.0723841
X-RAY DIFFRACTIONr_mcbond_other0.9033.0713840
X-RAY DIFFRACTIONr_mcangle_it1.6574.5944782
X-RAY DIFFRACTIONr_mcangle_other1.6574.5954783
X-RAY DIFFRACTIONr_scbond_it0.6923.1894257
X-RAY DIFFRACTIONr_scbond_other0.6923.1874254
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.2544.7376251
X-RAY DIFFRACTIONr_long_range_B_refined3.83124.5329551
X-RAY DIFFRACTIONr_long_range_B_other3.56224.3459310
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.799→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 366 -
Rwork0.312 6680 -
obs--68.59 %

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