+Open data
-Basic information
Entry | Database: PDB / ID: 2lcj | ||||||
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Title | Solution NMR structure of Pab PolII Intein | ||||||
Components | Pab polC intein | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information exodeoxyribonuclease I / single-stranded DNA 3'-5' DNA exonuclease activity / intein-mediated protein splicing / DNA catabolic process / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding Similarity search - Function | ||||||
Biological species | Pyrococcus abyssi (archaea) | ||||||
Method | SOLUTION NMR / simulated annealing, torsion angle dynamics | ||||||
Model details | closest to the average, model 1 | ||||||
Authors | Jiajing, L. / Mills, K.V. / Albracht, C.D. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Structural and Mutational Studies of a Hyperthermophilic Intein from DNA Polymerase II of Pyrococcus abyssi. Authors: Du, Z. / Liu, J. / Albracht, C.D. / Hsu, A. / Chen, W. / Marieni, M.D. / Colelli, K.M. / Williams, J.E. / Reitter, J.N. / Mills, K.V. / Wang, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2lcj.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2lcj.ent.gz | 977.7 KB | Display | PDB format |
PDBx/mmJSON format | 2lcj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lc/2lcj ftp://data.pdbj.org/pub/pdb/validation_reports/lc/2lcj | HTTPS FTP |
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-Related structure data
Similar structure data | |
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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: 21553.291 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus abyssi (archaea) / Strain: GE5 / Orsay / Gene: polC, PYRAB01200, PAB2404 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9V2F4, DNA-directed DNA polymerase |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: 3D 1H-13C NOESY aliphatic |
-Sample preparation
Details | Contents: 2 mM [U-100% 13C; U-100% 15N] protein, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O |
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Sample | Conc.: 2 mM / Component: protein-1 / Isotopic labeling: [U-100% 13C; U-100% 15N] |
Sample conditions | Ionic strength: 20 / pH: 6.5 / Pressure: ambient / Temperature: 320 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing, torsion angle dynamics / Software ordinal: 1 Details: xplor refinement with explicit water for final structure, structure model build. | ||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 20 |