+Open data
-Basic information
Entry | Database: PDB / ID: 2cjc | ||||||
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Title | Complexes of Dodecin with Flavin and Flavin-like Ligands | ||||||
Components | VNG1446H | ||||||
Keywords | FLAVOPROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | HALOBACTERIUM SALINARIUM (Halophile) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Grininger, M. / Seiler, F. / Zeth, K. / Oesterhelt, D. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: Dodecin Sequesters Fad in Closed Conformation from the Aqueous Solution. Authors: Grininger, M. / Seiler, F. / Zeth, K. / Oesterhelt, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cjc.cif.gz | 30.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cjc.ent.gz | 20.6 KB | Display | PDB format |
PDBx/mmJSON format | 2cjc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2cjc_validation.pdf.gz | 481.9 KB | Display | wwPDB validaton report |
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Full document | 2cjc_full_validation.pdf.gz | 482 KB | Display | |
Data in XML | 2cjc_validation.xml.gz | 3.3 KB | Display | |
Data in CIF | 2cjc_validation.cif.gz | 4.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cj/2cjc ftp://data.pdbj.org/pub/pdb/validation_reports/cj/2cjc | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 7442.059 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: FAD BOUND / Source: (gene. exp.) HALOBACTERIUM SALINARIUM (Halophile) / Strain: R1 / Description: GERMAN COLLECTION OF MICROORGANISMS (DSM 671) / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HPW4 |
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-Non-polymers , 6 types, 75 molecules
#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-SO4 / | #6: Chemical | ChemComp-FAD / | #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: 4.01 Å3/Da / Density % sol: 69.34 % |
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Crystal grow | pH: 7.5 Details: 0.2 M MGCL2, 2.0 M NACL, 0.1 M NA HEPES PH 7.5 AND 30% PEG400 |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0056 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 12, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0056 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→20 Å / Num. obs: 10961 / % possible obs: 99.1 % / Observed criterion σ(I): 2.5 / Redundancy: 6.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.85→1.96 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.67 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CRYSTALLIZATION OF RECONSTITUTED HOLOCOMPLEX
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.03 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→20 Å
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Refine LS restraints |
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