[English] 日本語
Yorodumi
- PDB-4f0e: Human ADP-RIBOSYLTRANSFERASE 7 (ARTD7/PARP15), CATALYTIC DOMAIN I... -

+
Open data


ID or keywords:

Loading...

-
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 / NAD+ poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / 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 / NAD+ poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / 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]

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more