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Yorodumi- PDB-1oko: Crystal structure of Pseudomonas Aeruginosa Lectin 1 complexed wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1oko | ||||||
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Title | Crystal structure of Pseudomonas Aeruginosa Lectin 1 complexed with galactose at 1.6 A resolution | ||||||
Components | PA-I GALACTOPHILIC LECTIN | ||||||
Keywords | SUGAR BINDING PROTEIN / GALACTOSE BINDING | ||||||
Function / homology | Function and homology information heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / carbohydrate binding / periplasmic space / cell surface / cytoplasm Similarity search - Function | ||||||
Biological species | PSEUDOMONAS AERUGINOSA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Cioci, G. / Mitchell, E. / Gautier, C. / Wimmerova, M. / Perez, S. / Gilboa-Garber, N. / Imberty, A. | ||||||
Citation | Journal: FEBS Lett. / Year: 2003 Title: Structural Basis of Calcium and Galactose Recognition by the Lectin Pa-Il of Pseudomonas Aeruginosa Authors: Cioci, G. / Mitchell, E. / Gautier, C. / Wimmerova, M. / Sudakevitz, D. / Perez, S. / Gilboa-Garber, N. / Imberty, A. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1oko.cif.gz | 114.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oko.ent.gz | 89.4 KB | Display | PDB format |
PDBx/mmJSON format | 1oko.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ok/1oko ftp://data.pdbj.org/pub/pdb/validation_reports/ok/1oko | HTTPS FTP |
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-Related structure data
Related structure data | 1uojC 1okpS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 12770.137 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) PSEUDOMONAS AERUGINOSA (bacteria) / References: UniProt: Q05097 |
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-Sugars , 2 types, 7 molecules
#3: Sugar | ChemComp-GAL / #6: Sugar | |
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-Non-polymers , 4 types, 490 molecules
#2: Chemical | ChemComp-CA / #4: Chemical | #5: Chemical | ChemComp-MPD / ( | #7: Water | ChemComp-HOH / | |
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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 Å3/Da / Density % sol: 37 % / Description: RFREE MERGED FROM EBI-13164 | ||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 5 Details: HANGING DROP: PROTEIN SOLUTION: PA1L 5 MG/ML, D-GAL 0.025 MG/ML, CACL2 & MGCL2 2MM RESERVOIR SOLUTION: (NH4)2SO4 1.5 M, PH 4.7, 5% MPD, 2% GLYCEROL 2 UL + 2 UL | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 4.7 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 15, 2003 / Details: MULTILAYER |
Radiation | Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→18.6 Å / Num. obs: 53762 / % possible obs: 94.9 % / Redundancy: 4.49 % / Biso Wilson estimate: 12.535 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 6.6701 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 4.23 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.42 / % possible all: 79.1 |
Reflection | *PLUS Highest resolution: 1.6 Å / Redundancy: 4.5 % / Num. measured all: 241596 / Rmerge(I) obs: 0.076 |
Reflection shell | *PLUS % possible obs: 79.1 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: MONOMER B FROM PREVIOULSY RESOLVED 1OKP Resolution: 1.6→18.602 Å / SU B: 1.779 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.09
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Displacement parameters | Biso mean: 11.301 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→18.602 Å
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Refinement | *PLUS Lowest resolution: 18.6 Å / Rfactor Rfree: 0.187 / Rfactor Rwork: 0.154 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.256 / Num. reflection Rfree: 144 / Rfactor Rwork: 0.197 / Num. reflection Rwork: 3066 |