[English] 日本語
Yorodumi- PDB-3at7: Crystal structure of bacterial cell-surface alginate-binding prot... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3at7 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of bacterial cell-surface alginate-binding protein Algp7 | ||||||
Components | Alginate-binding flagellin | ||||||
Keywords | STRUCTURAL PROTEIN / two up-and-down four-helical bundles / alginate binding / alginate | ||||||
Function / homology | M75 peptidase, HXXE motif / EfeO/Algp7, imelysin-like domain / Imelysin-like domain / Imelysin-like domain superfamily / Imelysin / A middle domain of Talin 1 / Up-down Bundle / Mainly Alpha / Alginate-binding protein Function and homology information | ||||||
Biological species | Sphingomonas (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Maruyama, Y. / Ochiai, A. / Mikami, B. / Hashimoto, W. / Murata, K. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2011 Title: Crystal structure of bacterial cell-surface alginate-binding protein with an M75 peptidase motif. Authors: Maruyama, Y. / Ochiai, A. / Mikami, B. / Hashimoto, W. / Murata, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3at7.cif.gz | 112.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3at7.ent.gz | 87.3 KB | Display | PDB format |
PDBx/mmJSON format | 3at7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/at/3at7 ftp://data.pdbj.org/pub/pdb/validation_reports/at/3at7 | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Details | AUTHOR DETERMINED BIOLOGICAL UNIT: UNKNOWN |
-Components
#1: Protein | Mass: 31701.088 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sphingomonas (bacteria) / Strain: A1 / Gene: p7 / Plasmid: pET44a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q25C86 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.88 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 4.1 Details: 10% PEG 8000, 0.2M NaCl, 0.1M Sodium Citrate pH4.1, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 23, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 32186 / % possible obs: 99.9 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 34.5 |
Reflection shell | Resolution: 2.1→2.18 Å / Rmerge(I) obs: 0.305 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.915 / SU B: 4.529 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R Free: 0.188 / 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: 21.663 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.155 Å / Total num. of bins used: 20
|