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- PDB-3hkv: Human poly(ADP-ribose) polymerase 10, catalytic fragment in compl... -

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Basic information

Entry
Database: PDB / ID: 3hkv
TitleHuman poly(ADP-ribose) polymerase 10, catalytic fragment in complex with an inhibitor 3-aminobenzamide
ComponentsPoly [ADP-ribose] polymerase 10
KeywordsTRANSFERASE / PARP / POLY(ADP-RIBOSE) POLYMERASE / NAD / Structural Genomics / Structural Genomics Consortium / SGC / Cytoplasm / Glycosyltransferase / Nucleus / Phosphoprotein / Polymorphism
Function / homology
Function and homology information


negative regulation of protein K63-linked ubiquitination / NAD+-protein-lysine ADP-ribosyltransferase activity / nicotinate metabolic process / Maturation of nucleoprotein / Nicotinate metabolism / protein auto-ADP-ribosylation / Maturation of nucleoprotein / K63-linked polyubiquitin modification-dependent protein binding / NAD+-protein-aspartate ADP-ribosyltransferase activity / protein poly-ADP-ribosylation ...negative regulation of protein K63-linked ubiquitination / NAD+-protein-lysine ADP-ribosyltransferase activity / nicotinate metabolic process / Maturation of nucleoprotein / Nicotinate metabolism / protein auto-ADP-ribosylation / Maturation of nucleoprotein / K63-linked polyubiquitin modification-dependent protein binding / 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 / negative regulation of fibroblast proliferation / nucleotidyltransferase activity / translesion synthesis / negative regulation of canonical NF-kappaB signal transduction / transcription corepressor activity / chromatin organization / DNA-binding transcription factor binding / viral protein processing / negative regulation of gene expression / DNA repair / nucleolus / nucleus / cytosol / cytoplasm
Similarity search - Function
PARP-10, RNA recognition motif 1 and 2 / Protein mono-ADP-ribosyltransferase PARP10, KH-domain type I / PARP14, third RRM 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. / Nucleotide-binding alpha-beta plait domain superfamily ...PARP-10, RNA recognition motif 1 and 2 / Protein mono-ADP-ribosyltransferase PARP10, KH-domain type I / PARP14, third RRM 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. / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
3-aminobenzamide / PHOSPHATE ION / Protein mono-ADP-ribosyltransferase PARP10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKarlberg, T. / Moche, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. ...Karlberg, T. / Moche, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Kotenyova, T. / Kotzsch, A. / Nielsen, T.K. / Nordlund, P. / Nyman, T. / Persson, C. / Roos, A.K. / Sagemark, J. / Schutz, P. / Siponen, M.I. / Thorsell, A.G. / Tresaugues, L. / Van Den Berg, S. / Weigelt, J. / Welin, M. / Wisniewska, M. / Schuler, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Human Poly(Adp-Ribose) Polymerase 10, Catalytic Fragment in Complex with an Inhibitor 3-Aminobenzamide
Authors: Karlberg, T. / Moche, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, ...Authors: Karlberg, T. / Moche, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Kotenyova, T. / Kotzsch, A. / Nielsen, T.K. / Nordlund, P. / Nyman, T. / Persson, C. / Roos, A.K. / Sagemark, J. / Schutz, P. / Siponen, M.I. / Thorsell, A.G. / Tresaugues, L. / Van Den Berg, S. / Weigelt, J. / Welin, M. / Wisniewska, M. / Schuler, H.
History
DepositionMay 26, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 23, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Poly [ADP-ribose] polymerase 10
B: Poly [ADP-ribose] polymerase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5659
Polymers48,9612
Non-polymers6037
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-45 kcal/mol
Surface area18220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.380, 97.380, 121.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Poly [ADP-ribose] polymerase 10 / PARP-10


Mass: 24480.705 Da / Num. of mol.: 2 / Fragment: catalytic domain, UNP residues 809-1017 / Mutation: R922K, V979M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARP10 / Plasmid: pNIC-CH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) R3 pRARE / References: UniProt: Q53GL7, NAD+ ADP-ribosyltransferase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-3AB / 3-aminobenzamide


Mass: 136.151 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8N2O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.93 Å3/Da / Density % sol: 58.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.49M NaH2PO4, 0.9M K2HPO4, pH7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 12, 2009 / Details: Rh-coated Si mirrors
RadiationMonochromator: Si (111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 34589 / Num. obs: 34589 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Rmerge(I) obs: 0.093 / Rsym value: 0.089 / Net I/σ(I): 15.3
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 8 % / Rmerge(I) obs: 0.722 / Mean I/σ(I) obs: 4 / Num. unique all: 2499 / Rsym value: 0.428 / % possible all: 99.4

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
REFMAC5.5.0035refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BLJ

3blj


Resolution: 2.1→29.84 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.189 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.172 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24196 1730 5 %RANDOM
Rwork0.19574 ---
all0.19801 32856 --
obs0.19801 32856 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.05 Å20 Å20 Å2
2--1.05 Å20 Å2
3----2.1 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3086 0 37 183 3306
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0213196
X-RAY DIFFRACTIONr_bond_other_d0.0010.022245
X-RAY DIFFRACTIONr_angle_refined_deg1.5061.9584343
X-RAY DIFFRACTIONr_angle_other_deg0.9173.0025355
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8825389
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.7621.557167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.17215504
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8661545
X-RAY DIFFRACTIONr_chiral_restr0.0970.2461
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213614
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02734
X-RAY DIFFRACTIONr_mcbond_it0.9861.51923
X-RAY DIFFRACTIONr_mcbond_other0.2141.5770
X-RAY DIFFRACTIONr_mcangle_it1.88323110
X-RAY DIFFRACTIONr_scbond_it2.69131273
X-RAY DIFFRACTIONr_scangle_it4.6284.51229
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 125 -
Rwork0.243 2363 -
obs-2488 100 %

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