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Yorodumi- PDB-2l8r: Solution structure of human protein C6orf130 in complex with ADP-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2l8r | ||||||
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Title | Solution structure of human protein C6orf130 in complex with ADP-ribose | ||||||
Components | Uncharacterized protein C6orf130 | ||||||
Keywords | HYDROLASE / macro domain / Structural Genomics / Protein Structure Initiative / PSI-2 / Center for Eukaryotic Structural Genomics / CESG / DEACYLASE | ||||||
Function / homology | Function and homology information ADP-ribosylglutamate hydrolase activity / protein de-ADP-ribosylation / peptidyl-glutamate ADP-deribosylation / purine nucleoside metabolic process / purine nucleoside binding / 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 ...ADP-ribosylglutamate hydrolase activity / protein de-ADP-ribosylation / peptidyl-glutamate ADP-deribosylation / purine nucleoside metabolic process / purine nucleoside binding / 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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION 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 details | lowest energy, model 1 | ||||||
Authors | Lytle, B.L. / Peterson, F.C. / Volkman, B.F. / Center for Eukaryotic Structural Genomics (CESG) | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2l8r.cif.gz | 1008.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2l8r.ent.gz | 846.8 KB | Display | PDB format |
PDBx/mmJSON format | 2l8r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2l8r_validation.pdf.gz | 502.8 KB | Display | wwPDB validaton report |
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Full document | 2l8r_full_validation.pdf.gz | 625.8 KB | Display | |
Data in XML | 2l8r_validation.xml.gz | 72.8 KB | Display | |
Data in CIF | 2l8r_validation.cif.gz | 89.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l8/2l8r ftp://data.pdbj.org/pub/pdb/validation_reports/l8/2l8r | HTTPS FTP |
-Related structure data
Related structure data | 2lgrC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | 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 |
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#2: Chemical | ChemComp-APR / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.75 mM [U-100% 13C; U-100% 15N] C6orf130, 93% H2O, 7% D2O Solvent system: 93% H2O/7% D2O |
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Sample | Conc.: 0.75 mM / Component: C6orf130-1 / Isotopic labeling: [U-100% 13C; U-100% 15N] |
Sample conditions | Ionic strength: 200 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | 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 ...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 constraints | NOE 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 representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 |