+Open data
-Basic information
Entry | Database: PDB / ID: 2cif | ||||||
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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: 2.8 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 | 2cif.cif.gz | 28.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cif.ent.gz | 19.7 KB | Display | PDB format |
PDBx/mmJSON format | 2cif.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2cif_validation.pdf.gz | 865.5 KB | Display | wwPDB validaton report |
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Full document | 2cif_full_validation.pdf.gz | 870.8 KB | Display | |
Data in XML | 2cif_validation.xml.gz | 6.4 KB | Display | |
Data in CIF | 2cif_validation.cif.gz | 7.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ci/2cif ftp://data.pdbj.org/pub/pdb/validation_reports/ci/2cif | HTTPS FTP |
-Related structure data
Related structure data | 2cieC 2cjcC 2cc9S 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 CRYSTALS SOAKED WITH FAD / 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, 18 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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-Details
Sequence details | PIR-NREF |
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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: 3.98 Å3/Da / Density % sol: 68.87 % |
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Crystal grow | pH: 7.5 Details: 0.1 M TRIS-HCL, 8% W/V PEG 8000 (8.5), 2.3 M NACL, pH 7.50 |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9168 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 20, 2003 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9168 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. obs: 32836 / % possible obs: 98.8 % / Observed criterion σ(I): 3.5 / Redundancy: 10 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 16.31 |
Reflection shell | Resolution: 2.8→2.97 Å / Redundancy: 10.32 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 3.64 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CC9 Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.864 / Cross valid method: THROUGHOUT / ESU R: 0.467 / ESU R Free: 0.341 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 36.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
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Refine LS restraints |
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