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- PDB-2lgr: Solution structure of human protein C6orf130, a putative macro domain -

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Basic information

Entry
Database: PDB / ID: 2lgr
TitleSolution structure of human protein C6orf130, a putative macro domain
ComponentsUncharacterized protein C6orf130
KeywordsHYDROLASE / macro domain / A1pp domain / Structural Genomics / Protein Structure Initiative / PSI / 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
ADP-ribose glycohydrolase OARD1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, molecular dynamics
Model detailslowest energy, model 1
AuthorsVolkman, B.F. / Lytle, B.L. / Peterson, F.C. / 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
DepositionAug 1, 2011Deposition site: BMRB / Processing site: RCSB
SupersessionAug 17, 2011ID: 2JYC
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2011Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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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)18,0471
Polymers18,0471
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 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Uncharacterized protein C6orf130


Mass: 18046.740 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BC011709.2, C6orf130 / Production host: CELL-FREE SYNTHESIS (others) / References: UniProt: Q9Y530

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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 13C-F1-Filtered 13C-F3 separated NOESY

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Sample preparation

DetailsContents: 0.55 mM [U-100% 13C; U-100% 15N] C6orf130, 20 mM BisTris, 200 mM sodium chloride, 2 mM DTT, 7 % [U-100% 2H] D2O, 93 % H2O, 93% H2O, 7% D2O
Solvent system: 93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.55 mMC6orf130-1[U-100% 13C; U-100% 15N]1
20 mMBisTris-21
200 mMsodium chloride-31
2 mMDTT-41
7 %D2O-5[U-100% 2H]1
93 %H2O-61
Sample conditionsIonic strength: 200 / pH: 6.5 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Xplor-NIH2.23SCHWIETERS,C.D.,KUSZEWSKI,J.J.,TJANDRA,N.,CLORE,G.M.refinement
TopSpin1.3Brukercollection
NMRPipe2006Delagio,F. et al.processing
XEASY1.3Eccles, C., Guntert, P., Billeter, M., Wuthrich, K.data analysis
GARANT2.1C. Bartelsdata analysis
CYANA3Guntert, P.structural calculation
CYANASCHWIETERS,C.D.,KUSZEWSKI,J.J.,TJANDRA,N.,CLORE,G.M.refinement
RefinementMethod: torsion angle dynamics, molecular dynamics / Software ordinal: 1
Details: AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT AND ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT. STRUCTURES ARE ...Details: AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT AND ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT. STRUCTURES ARE BASED ON A TOTAL OF 1971 NOE CONSTRAINTS (758 INTRA, 418 SEQUENTIAL, 238 MEDIUM and 557 LONG RANGE CONSTRAINTS) AND 180 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS., STRUCTURES ARE BASED ON A TOTAL OF 1971 NOE CONSTRAINTS (758 INTRA, 418 SEQUENTIAL, 238 MEDIUM and 557 LONG RANGE CONSTRAINTS) AND 180 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS.
NMR constraintsNOE constraints total: 1971 / NOE intraresidue total count: 758 / NOE long range total count: 557 / NOE medium range total count: 238 / NOE sequential total count: 418 / Protein phi angle constraints total count: 90 / Protein psi angle constraints total count: 90
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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