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- PDB-4f0e: Human ADP-RIBOSYLTRANSFERASE 7 (ARTD7/PARP15), CATALYTIC DOMAIN I... -

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Basic information

Entry
Database: PDB / ID: 4f0e
TitleHuman ADP-RIBOSYLTRANSFERASE 7 (ARTD7/PARP15), CATALYTIC DOMAIN IN COMPLEX WITH STO1102
ComponentsPoly [ADP-ribose] polymerase 15
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / ARTD / PARP / POLY (ADP-RIBOSE) POLYMERASE / ADP-RIBOSE / BAL3 / B-AGGRESSIVE LYMPHOMA PROTEIN 3 / TRANSFERASE / GLYCOSYLTRANSFERASE / NUCLEUS / TRANSCRIPTION / TRANSCRIPTION REGULATION / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


NAD+-protein-aspartate ADP-ribosyltransferase activity / protein poly-ADP-ribosylation / NAD+-protein-glutamate ADP-ribosyltransferase activity / NAD+-protein mono-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ poly-ADP-ribosyltransferase activity / NAD+ binding / nucleotidyltransferase activity / transcription corepressor activity / negative regulation of gene expression ...NAD+-protein-aspartate ADP-ribosyltransferase activity / protein poly-ADP-ribosylation / NAD+-protein-glutamate ADP-ribosyltransferase activity / NAD+-protein mono-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ poly-ADP-ribosyltransferase activity / NAD+ binding / nucleotidyltransferase activity / transcription corepressor activity / negative regulation of gene expression / negative regulation of transcription by RNA polymerase II / nucleus / cytoplasm
Similarity search - Function
: / Phosphoenolpyruvate Carboxykinase; domain 3 - #10 / Phosphoenolpyruvate Carboxykinase; domain 3 / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain ...: / Phosphoenolpyruvate Carboxykinase; domain 3 - #10 / Phosphoenolpyruvate Carboxykinase; domain 3 / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain / Macro domain-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-0RU / Protein mono-ADP-ribosyltransferase PARP15
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKarlberg, T. / Andersson, C.D. / Lindgren, A. / Thorsell, A.G. / Ekblad, T. / Spjut, S. / Weigelt, J. / Elofsson, M. / Linusson, A. / Schuler, H.
CitationJournal: J.Med.Chem. / Year: 2012
Title: Discovery of Ligands for ADP-Ribosyltransferases via Docking-Based Virtual Screening.
Authors: Andersson, C.D. / Karlberg, T. / Ekblad, T. / Lindgren, A.E. / Thorsell, A.G. / Spjut, S. / Uciechowska, U. / Niemiec, M.S. / Wittung-Stafshede, P. / Weigelt, J. / Elofsson, M. / Schuler, H. / Linusson, A.
History
DepositionMay 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Sep 13, 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 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 29, 2024Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly_prop.biol_id / _pdbx_struct_oper_list.matrix[1][1] ..._pdbx_struct_assembly_prop.biol_id / _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[3][3] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[2] / _pdbx_struct_oper_list.vector[3]

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Poly [ADP-ribose] polymerase 15
B: Poly [ADP-ribose] polymerase 15
C: Poly [ADP-ribose] polymerase 15
D: Poly [ADP-ribose] polymerase 15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,7247
Polymers91,8714
Non-polymers8533
Water1,49583
1
A: Poly [ADP-ribose] polymerase 15
hetero molecules

D: Poly [ADP-ribose] polymerase 15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5044
Polymers45,9362
Non-polymers5692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_544-x,y-1/2,-z-11
Buried area2050 Å2
ΔGint-8 kcal/mol
Surface area18530 Å2
MethodPISA
2
B: Poly [ADP-ribose] polymerase 15

C: Poly [ADP-ribose] polymerase 15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2203
Polymers45,9362
Non-polymers2841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area2180 Å2
ΔGint-9 kcal/mol
Surface area18690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.676, 45.383, 123.389
Angle α, β, γ (deg.)90.00, 90.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Poly [ADP-ribose] polymerase 15 / PARP-15 / B-aggressive lymphoma protein 3


Mass: 22967.785 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAL3, PARP15 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)R3 pRARE / References: UniProt: Q460N3, NAD+ ADP-ribosyltransferase
#2: Chemical ChemComp-0RU / 8-methyl-2-[(pyrimidin-2-ylsulfanyl)methyl]quinazolin-4(1H)-one


Mass: 284.336 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H12N4OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.12 Å3/Da / Density % sol: 42.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 10.5
Details: 40% 2-methyl-1,3-propanediol, 0.1 M CAPS, 2mM STO1102, pH 10.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93928 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 12, 2010 / Details: mirrors
RadiationMonochromator: channel cut ESRF monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93928 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. all: 30110 / Num. obs: 30110 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.159 / Net I/σ(I): 9.1
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.692 / Mean I/σ(I) obs: 3.8 / Num. unique all: 1988 / % possible all: 91.1

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7_650)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BLJ

3blj


Resolution: 2.4→38.028 Å / σ(F): 0 / σ(I): 0 / Phase error: 29.76 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2866 2020 6.71 %RANDOM
Rwork0.2198 ---
all0.2241 30110 --
obs0.2241 30110 98.14 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.956 Å2 / ksol: 0.391 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.2183 Å2-0 Å20.7898 Å2
2---18.9609 Å2-0 Å2
3---26.1792 Å2
Refinement stepCycle: LAST / Resolution: 2.4→38.028 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6305 0 53 83 6441
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036537
X-RAY DIFFRACTIONf_angle_d0.8658868
X-RAY DIFFRACTIONf_dihedral_angle_d15.6652379
X-RAY DIFFRACTIONf_chiral_restr0.06925
X-RAY DIFFRACTIONf_plane_restr0.0041155
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.4-2.46030.39621280.34641799192785
2.4603-2.52680.38511450.3022049219493
2.5268-2.60110.34861420.29441979212193
2.6011-2.68510.33131410.27892054219593
2.6851-2.7810.30161470.26841995214292
2.781-2.89230.31181410.25252010215193
2.8923-3.02390.33351470.24952047219493
3.0239-3.18320.31191410.22162006214793
3.1832-3.38250.25471450.20912018216393
3.3825-3.64340.25221430.1872038218193
3.6434-4.00960.23631420.18962018216093
4.0096-4.58880.24141440.16462054219892
4.5888-5.77730.2881500.19472011216191
5.7773-35.48960.291430.22592026216988

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