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- PDB-5h6j: DNA targeting ADP-ribosyltransferase Pierisin-1 in complex with b... -

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Basic information

Entry
Database: PDB / ID: 5h6j
TitleDNA targeting ADP-ribosyltransferase Pierisin-1 in complex with beta-NAD+
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Pierisin / Pierisin
Similarity search - Component
Biological speciesPieris rapae (cabbage white)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
A: Pierisin-1
B: Pierisin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7914
Polymers62,4642
Non-polymers1,3272
Water5,224290
1
A: Pierisin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8952
Polymers31,2321
Non-polymers6631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-6 kcal/mol
Surface area11280 Å2
MethodPISA
2
B: Pierisin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8952
Polymers31,2321
Non-polymers6631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-5 kcal/mol
Surface area11270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.328, 93.328, 120.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Pierisin-1


Mass: 31232.014 Da / Num. of mol.: 2 / Fragment: UNP residues 1-233 / Mutation: Q165E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pieris rapae (cabbage white) / Plasmid: pET32a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): pLysS
References: UniProt: H3JU00, UniProt: Q9U8Q4*PLUS, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / 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: 2.1 Å3/Da / Density % sol: 41.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M NaF, 6-10% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 20, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→43.52 Å / Num. obs: 42294 / % possible obs: 98.9 % / Redundancy: 13.1 % / Net I/σ(I): 20.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→41.738 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.905 / SU B: 5.088 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.211 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27991 2081 5 %RANDOM
Rwork0.26327 ---
obs0.26408 39720 98.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.446 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.9→41.738 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3641 0 88 290 4019
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193840
X-RAY DIFFRACTIONr_bond_other_d0.0010.023546
X-RAY DIFFRACTIONr_angle_refined_deg1.0281.965258
X-RAY DIFFRACTIONr_angle_other_deg0.88138096
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3485440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.08622.8200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.52615593
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.6561545
X-RAY DIFFRACTIONr_chiral_restr0.0590.2557
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214337
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02982
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_it0.4323.0841769
X-RAY DIFFRACTIONr_mcbond_other0.4323.0831768
X-RAY DIFFRACTIONr_mcangle_it0.8274.6212206
X-RAY DIFFRACTIONr_mcangle_other0.8264.6232207
X-RAY DIFFRACTIONr_scbond_it0.1773.2352071
X-RAY DIFFRACTIONr_scbond_other0.1783.2362072
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.3894.843053
X-RAY DIFFRACTIONr_long_range_B_refined3.14825.734592
X-RAY DIFFRACTIONr_long_range_B_other2.92125.4864472
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 104 -
Rwork0.348 2388 -
obs--80.67 %

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