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- PDB-2eee: Solution structure of the A1pp domain from human protein C6orf130 -

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Basic information

Entry
Database: PDB / ID: 2eee
TitleSolution structure of the A1pp domain from human protein C6orf130
ComponentsUncharacterized protein C6orf130
KeywordsGENE REGULATION / Macro domain / A1pp domain / ADP-ribose binding / Rossmann fold / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


peptidyl-glutamate ADP-deribosylation / ADP-ribosylglutamate hydrolase activity / protein de-ADP-ribosylation / O-acetyl-ADP-ribose deacetylase activity / purine nucleoside binding / purine nucleoside metabolic process / 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 ...peptidyl-glutamate ADP-deribosylation / ADP-ribosylglutamate hydrolase activity / protein de-ADP-ribosylation / O-acetyl-ADP-ribose deacetylase activity / purine nucleoside binding / purine nucleoside metabolic process / 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 / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADP-ribose glycohydrolase OARD1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, restrained molecular dynamics
AuthorsTomizawa, T. / Koshiba, S. / Watanabe, S. / Harada, T. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the A1pp domain from human protein C6orf130
Authors: Tomizawa, T. / Koshiba, S. / Watanabe, S. / Harada, T. / Kigawa, T. / Yokoyama, S.
History
DepositionFeb 15, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
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
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein C6orf130


Theoretical massNumber of molelcules
Total (without water)16,4951
Polymers16,4951
Non-polymers00
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 / 100structures with the least restraint violations,structures with the lowest energy, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Uncharacterized protein C6orf130 / Protein C6orf130


Mass: 16495.072 Da / Num. of mol.: 1 / Fragment: A1pp domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: C6orf130 / Plasmid: P060821-05 / References: UniProt: Q9Y530

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY

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Sample preparation

DetailsContents: 1.22mM A1pp domain U-15N,13C; 20mM d-Tris-HCl(pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 296 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
NMRPipe20060524Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.9823Kobayashi, N.data analysis
CYANA2.0.17Guntert, P.structure solution
CYANA2.0.17Guntert, P.refinement
RefinementMethod: torsion angle dynamics, restrained molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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