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- PDB-2lgr: Solution structure of human protein C6orf130, a putative macro domain -
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Open data
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Basic information
Entry | Database: PDB / ID: 2lgr | |||||||||
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Title | Solution structure of human protein C6orf130, a putative macro domain | |||||||||
![]() | Uncharacterized protein C6orf130 | |||||||||
![]() | HYDROLASE / macro domain / A1pp domain / Structural Genomics / Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics / CESG / DEACYLASE | |||||||||
Function / homology | ![]() 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 | ![]() | |||||||||
Method | SOLUTION NMR / torsion angle dynamics, molecular dynamics | |||||||||
Model details | lowest energy, model 1 | |||||||||
![]() | Volkman, B.F. / Lytle, B.L. / Peterson, F.C. / Center for Eukaryotic Structural Genomics (CESG) | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1 MB | Display | ![]() |
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PDB format | ![]() | 902.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein | Mass: 18046.740 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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Sample preparation
Details | Contents: 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 | ||||||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 200 / pH: 6.5 / Pressure: AMBIENT / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz |
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Processing
NMR software |
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Refinement | Method: 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 constraints | NOE 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 representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 |