+Open data
-Basic information
Entry | Database: PDB / ID: 1mog | ||||||
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Title | Crystal structure of H. salinarum dodecin | ||||||
Components | Dodecin | ||||||
Keywords | UNKNOWN FUNCTION / binding site for dimerized riboflavin / 23-symmetric dodecamer | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Halobacterium salinarum (Halophile) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.7 Å | ||||||
Authors | Bieger, B. / Essen, L.-O. / Oesterhelt, D. | ||||||
Citation | Journal: Structure / Year: 2003 Title: Crystal Structure of Halophilic Dodecin: A Novel, Dodecameric Flavin Binding Protein from Halobacterium salinarum Authors: Bieger, B. / Essen, L.-O. / Oesterhelt, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mog.cif.gz | 30.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mog.ent.gz | 21.6 KB | Display | PDB format |
PDBx/mmJSON format | 1mog.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mo/1mog ftp://data.pdbj.org/pub/pdb/validation_reports/mo/1mog | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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Details | The biological assembly is a dodecamer generated from the monomer in the asymmetric unit by the operations: X,Y,Z Z,X,Y Y,Z,X -X,-Y,Z -Z,-X,Y -Y,-Z,X X,-Y,-Z Z,-X,-Y Y,-Z,-X -X,Y,-Z -Z,X,-Y -Y,Z,-X |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 7310.863 Da / Num. of mol.: 1 / Fragment: residues 10-77 / Source method: isolated from a natural source / Source: (natural) Halobacterium salinarum (Halophile) / References: UniProt: Q9HPW4 |
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-Non-polymers , 5 types, 104 molecules
#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Chemical | #5: Chemical | ChemComp-RBF / | #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: 4.07 Å3/Da / Density % sol: 69.78 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 400, magnesium chloride, sodium chloride, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.933 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 12, 2000 / Details: mirrors |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→20 Å / Num. all: 14027 / Num. obs: 14027 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.3 % / Biso Wilson estimate: 22.5 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 38.3 |
Reflection shell | Resolution: 1.7→1.72 Å / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 2.6 / % possible all: 99.9 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 116286 |
Reflection shell | *PLUS % possible obs: 99.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.7→14.88 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 63.0684 Å2 / ksol: 0.445967 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→14.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 15 Å / % reflection Rfree: 9 % / Rfactor Rwork: 0.18 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.214 |