+Open data
-Basic information
Entry | Database: PDB / ID: 2cc9 | ||||||
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Title | Complexes of Dodecin with Flavin and Flavin-like Ligands | ||||||
Components | VNG1446H | ||||||
Keywords | FLAVOPROTEIN / FLAVIN / FLAVIN-LIKE LIGANDS | ||||||
Function / homology | Function and homology information | ||||||
Biological species | HALOBACTERIUM SALINARUM (Halophile) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Grininger, M. / Zeth, K. / Oesterhelt, D. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: Dodecins: A Family of Lumichrome Binding Proteins. Authors: Grininger, M. / 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 | 2cc9.cif.gz | 28.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cc9.ent.gz | 19.6 KB | Display | PDB format |
PDBx/mmJSON format | 2cc9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cc/2cc9 ftp://data.pdbj.org/pub/pdb/validation_reports/cc/2cc9 | HTTPS FTP |
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-Related structure data
Related structure data | 2cc6SC 2cc7C 2cc8C 2ccbC 2cccC 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 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: APOPROTEIN / Source: (gene. exp.) HALOBACTERIUM SALINARUM (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, UniProt: B0R5M0*PLUS |
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-Non-polymers , 5 types, 85 molecules
#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-SO4 / | #6: 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: 4.05 Å3/Da / Density % sol: 69.6 % |
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Crystal grow | pH: 7.5 / Details: pH 7.50 |
-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 25, 2004 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→20 Å / Num. obs: 151983 / % possible obs: 99.8 % / Observed criterion σ(I): 4.1 / Redundancy: 8.2 % / Rmerge(I) obs: 0.01 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 1.55→1.64 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 4.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CC6 Resolution: 1.55→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.945 / SU B: 0.991 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.064 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.23 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→20 Å
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Refine LS restraints |
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