+Open data
-Basic information
Entry | Database: PDB / ID: 4b2m | |||||||||
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Title | COMPLEXES OF DODECIN WITH FLAVIN AND FLAVIN-LIKE LIGANDS | |||||||||
Components | DODECIN | |||||||||
Keywords | FLAVOPROTEIN / INCORPORATION OF ARTIFICIAL (NON-CANONICAL) AMINO ACIDS / PROTEIN REACTION CONTROL | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | HALOBACTERIUM SALINARUM (Halophile) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Staudt, H. / Hoesl, M. / Dreuw, A. / Serdjukow, S. / Oesterhelt, D. / Budisa, N. / Wachtveitl, J. / Grininger, M. | |||||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2013 Title: The flavoprotein dodecin as a redox probe for electron transfer through DNA. Authors: Yu, Y. / Heidel, B. / Parapugna, T.L. / Wenderhold-Reeb, S. / Song, B. / Schonherr, H. / Grininger, M. / Noll, G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4b2m.cif.gz | 31.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4b2m.ent.gz | 21.3 KB | Display | PDB format |
PDBx/mmJSON format | 4b2m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b2/4b2m ftp://data.pdbj.org/pub/pdb/validation_reports/b2/4b2m | HTTPS FTP |
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-Related structure data
Related structure data | 4b2hC 2cccS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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: 8514.200 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: TRYPTOPHAN 36 EXCHANGED BY 4AZATRYPTOPHAN, RIBOFLAVIN BOUND Source: (gene. exp.) HALOBACTERIUM SALINARUM (Halophile) / Strain: R1 / Description: GERMAN COLLECTION OF MICROORGANISMS (DSM 671) / Plasmid: PQE80L / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: B0R5M0 |
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-Non-polymers , 6 types, 76 molecules
#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-SO4 / | #6: Chemical | ChemComp-RBF / | #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: 3.64 Å3/Da / Density % sol: 66 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 0.1 M HEPES (PH 7.5), PEG 400 30% (V/V), 2.5 M NACL, 0.2 M MGCL2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 20, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 8867 / % possible obs: 99.8 % / Observed criterion σ(I): 4 / Redundancy: 13.8 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 4.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CCC Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.288 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 27.392 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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