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Yorodumi- PDB-4bei: V. cholera biofilm scaffolding protein RbmA in complex with 18-cr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bei | ||||||
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Title | V. cholera biofilm scaffolding protein RbmA in complex with 18-crown- 6 | ||||||
Components | RBMA | ||||||
Keywords | CELL ADHESION / BACTERIAL COMMUNITY | ||||||
Function / homology | Immunoglobulin-like - #3880 / Immunoglobulin-like / Sandwich / Mainly Beta / 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE / DI(HYDROXYETHYL)ETHER / : Function and homology information | ||||||
Biological species | VIBRIO CHOLERAE MJ-1236 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Maestre-Reyna, M. / Wang, A.H.-J. | ||||||
Citation | Journal: Plos One / Year: 2013 Title: Structural Insights Into Rbma, a Biofilm Scaffolding Protein of V. Cholerae. Authors: Maestre-Reyna, M. / Wu, W. / Wang, A.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bei.cif.gz | 365.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bei.ent.gz | 298.5 KB | Display | PDB format |
PDBx/mmJSON format | 4bei.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bei_validation.pdf.gz | 3.1 MB | Display | wwPDB validaton report |
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Full document | 4bei_full_validation.pdf.gz | 3.2 MB | Display | |
Data in XML | 4bei_validation.xml.gz | 69 KB | Display | |
Data in CIF | 4bei_validation.cif.gz | 90.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/be/4bei ftp://data.pdbj.org/pub/pdb/validation_reports/be/4bei | HTTPS FTP |
-Related structure data
Related structure data | 4be5SC 4be6C 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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Unit cell |
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-Components
#1: Protein | Mass: 28696.119 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) VIBRIO CHOLERAE MJ-1236 (bacteria) / Variant: SEROTYPE O1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C3NSJ9 #2: Chemical | ChemComp-O4B / #3: Chemical | ChemComp-PEG / #4: 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: 2.74 Å3/Da / Density % sol: 55.1 % / Description: NONE |
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Crystal grow | pH: 7 Details: 0.1 M HEPES PH 7 0.2 M CACL2 30 % (V/V) PEG 400 50 MM 18-CROWN-6 |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 15, 2012 / Details: MIRRORS |
Radiation | Monochromator: HORIZONTALLY FOCUSING SINGLE CRYSTAL MONOCHROMATOR Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97622 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→22 Å / Num. obs: 75002 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 21.6 |
Reflection shell | Resolution: 2.6→2.9 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.93 / Mean I/σ(I) obs: 2.44 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4BE5 Resolution: 2.6→21.96 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.918 / SU B: 12.154 / SU ML: 0.253 / Cross valid method: THROUGHOUT / ESU R: 0.624 / ESU R Free: 0.312 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 53.439 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→21.96 Å
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Refine LS restraints |
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