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Yorodumi- PDB-4uie: Crystal structure of the S-layer protein SbsC, domains 7, 8 and 9 -
+Open data
-Basic information
Entry | Database: PDB / ID: 4uie | ||||||
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Title | Crystal structure of the S-layer protein SbsC, domains 7, 8 and 9 | ||||||
Components | SURFACE LAYER PROTEIN | ||||||
Keywords | SUGAR BINDING PROTEIN / S-LAYER | ||||||
Function / homology | Function and homology information | ||||||
Biological species | GEOBACILLUS STEAROTHERMOPHILUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3.1 Å | ||||||
Authors | Pavkov-Keller, T. / Dordic, A. / Egelseer, E.M. / Sleytr, U.B. / Keller, W. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the S-Layer Protein Sbsc Authors: Pavkov-Keller, T. / Dordic, A. / Eder, M. / Davies, K. / Mills, D. / Egelseer, E.M. / Sleytr, U.B. / Kuehlbrandt, W. / Vonck, J. / Keller, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4uie.cif.gz | 71.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uie.ent.gz | 56.1 KB | Display | PDB format |
PDBx/mmJSON format | 4uie.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ui/4uie ftp://data.pdbj.org/pub/pdb/validation_reports/ui/4uie | HTTPS FTP |
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-Related structure data
Related structure data | |
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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
#1: Protein | Mass: 35299.309 Da / Num. of mol.: 1 / Fragment: DOMAINS 7,8 AND 9, RESIDUES 754-1099 Source method: isolated from a genetically manipulated source Source: (gene. exp.) GEOBACILLUS STEAROTHERMOPHILUS (bacteria) Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O68840 | ||||
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#2: Chemical | #3: Chemical | ChemComp-CA / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.9 Å3/Da / Density % sol: 68.4 % Description: 3 DIFFERENT CRYSTAL FORMS WERE AVAILABLE - P41211, P21212 AND P3121. THIS CRYSTAL IS THE ONLY ONE FOR THE FORM P3121 AND WAS PREPARED AS OS-DERIVATIVE. THE STRUCTURE WAS SOLVED BY SIRAS ...Description: 3 DIFFERENT CRYSTAL FORMS WERE AVAILABLE - P41211, P21212 AND P3121. THIS CRYSTAL IS THE ONLY ONE FOR THE FORM P3121 AND WAS PREPARED AS OS-DERIVATIVE. THE STRUCTURE WAS SOLVED BY SIRAS USING NATIVE AND AU- DERIVATIVE DATA OF ANISOTROPIC CRYSTAL FORM P41211. THIS INITIAL PHASES WERE USED AS STARTING POINT FOR DMMULTI. THE BEST ELECTRON DENSITY MAP WAS OBTAINED FROM THE DATA FROM P3121 CRYSTAL. THIS WAS ALSO THE ONLY FORM WHERE DOMAIN 9 WAS NICELY ORDERED AND THE SEQUENCE COULD BE PLACED IN THE ELECTRON DENSITY. 2 OS ATOMS THAT ARE PRESENT IN THE STRUCTURE SHOULD COME FROM THE SOAKING. NEVERTHELESS, THE STRUCTURE COULD NOT BE SOLVED BY SAD USING ONLY THIS DATA. CA ATOM PRESENT IN DOMAIN 7 IS ALSO PRESENT IN NATIVE STRUCTURES FROM OTHER FORMS. TWO OTHER FORMS WERE NOT FURTHER REFINED AND DEPOSITED WHILE DOMAIN 9 IS PARTIALLY DISORDERED. |
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Crystal grow | Details: CA. 5MG/ML PROTEIN CONC. 2-2.4M SODIUM MALONATE PH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9486 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 27, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9486 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→20 Å / Num. obs: 9719 / % possible obs: 91 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 3.1→3.15 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.1 / % possible all: 83.6 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS Starting model: NONE Resolution: 3.1→19.75 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.831 / SU B: 20.708 / SU ML: 0.358 / Cross valid method: THROUGHOUT / ESU R Free: 0.485 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. 3 DIFFERENT CRYSTAL FORMS WERE AVAILABLE - P41211, P21212 ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. 3 DIFFERENT CRYSTAL FORMS WERE AVAILABLE - P41211, P21212 AND P3121. THIS CRYSTAL IS THE ONLY ONE FOR THE FORM P3121. ONLY IN THIS FORM DOMAIN 9 WAS NICELY ORDERED AND THE SEQUENCE COULD BE PLACED IN ELECTRON DENSITY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.394 Å2
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Refinement step | Cycle: LAST / Resolution: 3.1→19.75 Å
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Refine LS restraints |
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