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Yorodumi- PDB-3td5: Crystal structure of OmpA-like domain from Acinetobacter baumanni... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3td5 | |||||||||
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Title | Crystal structure of OmpA-like domain from Acinetobacter baumannii in complex with L-Ala-gamma-D-Glu-m-DAP-D-Ala-D-Ala | |||||||||
Components |
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Keywords | MEMBRANE PROTEIN/PEPTIDE BINDING PROTEIN / OmpA-like fold / cell-wall attachment / peptidoglycan-binding / MEMBRANE PROTEIN-PEPTIDE BINDING PROTEIN complex | |||||||||
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: 2 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3td5.cif.gz | 226.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3td5.ent.gz | 182.9 KB | Display | PDB format |
PDBx/mmJSON format | 3td5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/td/3td5 ftp://data.pdbj.org/pub/pdb/validation_reports/td/3td5 | HTTPS FTP |
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-Related structure data
Related structure data | 3td3SC 3td4C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-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: Protein/peptide | Mass: 532.544 Da / Num. of mol.: 8 / Source method: obtained synthetically / Details: synthetic peptide #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | Compound details | THE PEPTIDOGLYCAN IN CHAINS I, J, K, L, M, N, O, P CORRESPONDS TO MURAMYL PENTAPEPTIDE. HOWEVER, ...THE PEPTIDOGLY | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.15 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES, 62.5%(v/v) 2-methyl-2,4-pentanediol , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 4, 2011 |
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: 2→81.3 Å / Num. obs: 78672 / % possible obs: 92.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2→2.11 Å / % possible all: 92.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3TD3 Resolution: 2→81.3 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Refinement step | Cycle: LAST / Resolution: 2→81.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å
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