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- PDB-2l8r: Solution structure of human protein C6orf130 in complex with ADP-... -

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Basic information

Entry
Database: PDB / ID: 2l8r
TitleSolution structure of human protein C6orf130 in complex with ADP-ribose
ComponentsUncharacterized protein C6orf130
KeywordsHYDROLASE / macro domain / Structural Genomics / Protein Structure Initiative / PSI-2 / Center for Eukaryotic Structural Genomics / CESG / DEACYLASE
Function / homology
Function and homology information


purine nucleoside binding / peptidyl-glutamate ADP-deribosylation / ADP-ribosylglutamate hydrolase activity / protein de-ADP-ribosylation / ADP-ribosyl-[dinitrogen reductase] hydrolase activity / purine nucleoside metabolic process / O-acetyl-ADP-ribose deacetylase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / site of DNA damage ...purine nucleoside binding / peptidyl-glutamate ADP-deribosylation / ADP-ribosylglutamate hydrolase activity / protein de-ADP-ribosylation / ADP-ribosyl-[dinitrogen reductase] hydrolase activity / purine nucleoside metabolic process / O-acetyl-ADP-ribose deacetylase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / site of DNA damage / DNA damage response / nucleolus / nucleoplasm
Similarity search - Function
: / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain / Macro domain-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5-DIPHOSPHORIBOSE / ADP-ribose glycohydrolase OARD1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT., torsion angle dynamics, AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT
Model detailslowest energy, model 1
AuthorsLytle, B.L. / Peterson, F.C. / Volkman, B.F. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Orphan Macrodomain Protein (Human C6orf130) Is an O-Acyl-ADP-ribose Deacylase: SOLUTION STRUCTURE AND CATALYTIC PROPERTIES.
Authors: Peterson, F.C. / Chen, D. / Lytle, B.L. / Rossi, M.N. / Ahel, I. / Denu, J.M. / Volkman, B.F.
History
DepositionJan 22, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 17, 2011Group: Structure summary
Revision 1.3Oct 26, 2011Group: Database references
Revision 1.4May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein C6orf130
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4642
Polymers16,9051
Non-polymers5591
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Uncharacterized protein C6orf130


Mass: 16904.506 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C6orf130 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009[pREP4] / References: UniProt: Q9Y530
#2: Chemical ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N5O14P2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
1313D 13C-separated NOESY (AROMATIC)
1413D F1-13C-flitered/F3-13C-edited 1H-13C NOESY aliphatic

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Sample preparation

DetailsContents: 0.75 mM [U-100% 13C; U-100% 15N] C6orf130, 93% H2O, 7% D2O
Solvent system: 93% H2O/7% D2O
SampleConc.: 0.75 mM / Component: C6orf130-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 200 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Xplor-NIH2.9.3SCHWIETERS,C.D.,KUSZEWSKI,J.J.,TJANDRA,N.,CLORE,G.M.refinement
TopSpin2.1Brukercollection
NMRPipe2007Delagio,F. et al.processing
XEASY1.3Eccles, C., Guntert, P., Billeter, M., Wuthrich, K.data analysis
GARANT2.1C. Bartelsdata analysis
CYANA2.1Guntert, P.structural calculation
CYANArefinement
RefinementMethod: AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT., torsion angle ...Method: AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT., torsion angle dynamics, AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT
Software ordinal: 1
Details: STRUCTURES ARE BASED ON A TOTAL OF 2020 NOE CONSTRAINTS (632 INTRA, 416 SEQUENTIAL, 303 MEDIUM, 630 LONG RANGE, and 39 INTERMOLECULAR CONSTRAINTS) AND 211 PHI AND PSI DIHEDRAL ANGLE ...Details: STRUCTURES ARE BASED ON A TOTAL OF 2020 NOE CONSTRAINTS (632 INTRA, 416 SEQUENTIAL, 303 MEDIUM, 630 LONG RANGE, and 39 INTERMOLECULAR CONSTRAINTS) AND 211 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS., STRUCTURES ARE BASED ON A TOTAL OF 2020 NOE CONSTRAINTS (632 INTRA, 416 SEQUENTIAL, 303 MEDIUM, 630 LONG RANGE, and 39 INTERMOLECULAR CONSTRAINTS) AND 211 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS.
NMR constraintsNOE constraints total: 2020 / NOE intraresidue total count: 632 / NOE long range total count: 630 / NOE medium range total count: 303 / NOE sequential total count: 416
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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