[English] 日本語
Yorodumi- PDB-2rn7: NMR solution structure of TnpE protein from Shigella flexneri. No... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2rn7 | ||||||
---|---|---|---|---|---|---|---|
Title | NMR solution structure of TnpE protein from Shigella flexneri. Northeast Structural Genomics Target SfR125 | ||||||
Components | IS629 orfA | ||||||
Keywords | UNKNOWN FUNCTION / helix / all alpha / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Shigella flexneri (bacteria) | ||||||
Method | SOLUTION NMR / DGSA-distance geometry simulated annealing, water refinement | ||||||
Model details | all alpha | ||||||
Authors | Ramelot, T.A. / Cort, J.R. / Semesi, A. / Garcia, M. / Yee, A.A. / Arrowsmith, C.H. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: NMR solution structure of TnpE protein from Shigella flexneri. Northeast Structural Genomics Target SfR125 Authors: Ramelot, T.A. / Cort, J.R. / Semesi, A. / Garcia, M. / Yee, A. / Arrowsmith, C.H. / Kennedy, M.A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2rn7.cif.gz | 691.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2rn7.ent.gz | 583.5 KB | Display | PDB format |
PDBx/mmJSON format | 2rn7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2rn7_validation.pdf.gz | 340.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2rn7_full_validation.pdf.gz | 464.2 KB | Display | |
Data in XML | 2rn7_validation.xml.gz | 31.4 KB | Display | |
Data in CIF | 2rn7_validation.cif.gz | 53.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rn/2rn7 ftp://data.pdbj.org/pub/pdb/validation_reports/rn/2rn7 | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein | Mass: 12662.289 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: tnpE / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 pMGK / References: UniProt: Q7UDG6, UniProt: A0A0H2VTH7*PLUS |
---|---|
Sequence details | THERE ARE CONFLICTS BETWEEN SEQRES(LEU A 92) AND SEQUENCE DATABASE (GLN). THE AUTHORS BELIEVE THAT ...THERE ARE CONFLICTS BETWEEN SEQRES(LEU A 92) AND SEQUENCE DATABASE (GLN). THE AUTHORS BELIEVE THAT THE SEQRES IS CORRECT AND IS THE TRUE IDENTITY OF THESE RESIDUES AND IS NATURAL MUTANT. |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR / Details: all alpha | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Details |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sample conditions | Ionic strength: 0.5 / pH: 7.7 / Pressure: ambient / Temperature: 293 K |
-NMR measurement
NMR spectrometer |
|
---|
-Processing
NMR software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: DGSA-distance geometry simulated annealing, water refinement Software ordinal: 1 / Details: Xplor-NIH, CNS | ||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 351 / NOE intraresidue total count: 9 / NOE long range total count: 89 / NOE medium range total count: 153 / NOE sequential total count: 109 / Hydrogen bond constraints total count: 38 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 41 / Protein psi angle constraints total count: 41 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 25 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 0.9 ° / Maximum upper distance constraint violation: 0.08 Å | ||||||||||||||||||||||||||||
NMR ensemble rms | Distance rms dev: 0.01 Å |