[English] 日本語
Yorodumi- PDB-3td4: Crystal structure of OmpA-like domain from Acinetobacter baumanni... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3td4 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of OmpA-like domain from Acinetobacter baumannii in complex with diaminopimelate | |||||||||
Components | Outer membrane protein omp38 | |||||||||
Keywords | MEMBRANE PROTEIN / PEPTIDE BINDING PROTEIN / OmpA-like fold / cell-wall attachment / peptidoglycan-binding | |||||||||
Function / homology | Function and homology information porin activity / pore complex / host cell mitochondrion / monoatomic ion transport / cell outer membrane Similarity search - Function | |||||||||
Biological species | Acinetobacter baumannii (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å | |||||||||
Authors | Park, J.S. / Lee, W.C. / Song, J.H. / Kim, H.Y. | |||||||||
Citation | Journal: Faseb J. / Year: 2012 Title: Mechanism of anchoring of OmpA protein to the cell wall peptidoglycan of the gram-negative bacterial outer membrane Authors: Park, J.S. / Lee, W.C. / Yeo, K.J. / Ryu, K.S. / Kumarasiri, M. / Hesek, D. / Lee, M. / Mobashery, S. / Song, J.H. / Kim, S.I. / Lee, J.C. / Cheong, C. / Jeon, Y.H. / Kim, H.Y. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3td4.cif.gz | 214.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3td4.ent.gz | 172.4 KB | Display | PDB format |
PDBx/mmJSON format | 3td4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3td4_validation.pdf.gz | 490.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3td4_full_validation.pdf.gz | 513.8 KB | Display | |
Data in XML | 3td4_validation.xml.gz | 46.9 KB | Display | |
Data in CIF | 3td4_validation.cif.gz | 63.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/td/3td4 ftp://data.pdbj.org/pub/pdb/validation_reports/td/3td4 | HTTPS FTP |
-Related structure data
Related structure data | 3td3SC 3td5C S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 13879.479 Da / Num. of mol.: 8 / Fragment: C-TERMINAL DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: omp38 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6RYW5 #2: Chemical | ChemComp-API / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.34 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1M Ammonium tartrate, 15%-20% PEG3350, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 24, 2009 |
Radiation | Monochromator: Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→94.86 Å / Num. obs: 93970 / % possible obs: 99.14 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3TD3 Resolution: 1.79→94.86 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.267 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.44 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.79→94.86 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.79→1.837 Å / Total num. of bins used: 20
|