+Open data
-Basic information
Entry | Database: PDB / ID: 2lqm | ||||||
---|---|---|---|---|---|---|---|
Title | Solution Structures of RadA intein from Pyrococcus horikoshii | ||||||
Components | Pho radA intein | ||||||
Keywords | UNKNOWN FUNCTION | ||||||
Function / homology | Function and homology information DNA recombinase assembly / mitotic recombination / DNA strand invasion / intein-mediated protein splicing / DNA strand exchange activity / ATP-dependent DNA damage sensor activity / single-stranded DNA binding / double-stranded DNA binding / damaged DNA binding / ATP binding Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | closest to the average, model 1 | ||||||
Authors | Oeemig, J.S. / Zhou, D. / Kajander, T. / Wlodawer, A. / Iwai, H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2012 Title: NMR and Crystal Structures of the Pyrococcus horikoshii RadA Intein Guide a Strategy for Engineering a Highly Efficient and Promiscuous Intein. Authors: Oeemig, J.S. / Zhou, D. / Kajander, T. / Wlodawer, A. / Iwai, H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2lqm.cif.gz | 1 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2lqm.ent.gz | 903.8 KB | Display | PDB format |
PDBx/mmJSON format | 2lqm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lq/2lqm ftp://data.pdbj.org/pub/pdb/validation_reports/lq/2lqm | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein | Mass: 19918.551 Da / Num. of mol.: 1 / Mutation: C1A, T173A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3 Gene: DNA repair and recombination protein RadA, PH0263, radA Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: O58001 |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Details | Contents: 0.4 mM [U-99% 13C; U-99% 15N] PhoRadA intein, 20 mM sodium phosphate, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample |
| ||||||||||||
Sample conditions | pH: 6 / Pressure: ambient / Temperature: 303 K |
-NMR measurement
NMR spectrometer |
|
---|
-Processing
NMR software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: simulated annealing / Software ordinal: 1 | ||||||||||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 3515 / NOE intraresidue total count: 688 / NOE long range total count: 1436 / NOE medium range total count: 425 / NOE sequential total count: 966 / Protein phi angle constraints total count: 136 / Protein psi angle constraints total count: 144 | ||||||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 12.26 ° / Maximum upper distance constraint violation: 0.67 Å | ||||||||||||||||||||||||||||||||||||
NMR ensemble rms | Distance rms dev: 0.0152 Å / Distance rms dev error: 0.0024 Å |