+Open data
-Basic information
Entry | Database: PDB / ID: 3a3b | ||||||
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Title | Crystal structure of LumP complexed with flavin mononucleotide | ||||||
Components | Lumazine protein | ||||||
Keywords | LUMINESCENT PROTEIN / luminous bacteria / lumazine protein / flavin mononucleotide | ||||||
Function / homology | Function and homology information riboflavin synthase / riboflavin synthase activity / riboflavin biosynthetic process / nucleotide binding Similarity search - Function | ||||||
Biological species | Photobacterium kishitanii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Sato, Y. | ||||||
Citation | Journal: J.Bacteriol. / Year: 2009 Title: Crystal structures of the lumazine protein from Photobacterium kishitanii in complexes with the authentic chromophore, 6,7-dimethyl-8-(1'-D-ribityl) lumazine and its analogues, riboflavin and ...Title: Crystal structures of the lumazine protein from Photobacterium kishitanii in complexes with the authentic chromophore, 6,7-dimethyl-8-(1'-D-ribityl) lumazine and its analogues, riboflavin and FMN, at high resolution Authors: Sato, Y. / Shimizu, S. / Ohtaki, A. / Noguchi, K. / Miyatake, H. / Dohmae, N. / Sasaki, S. / Odaka, M. / Yohda, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3a3b.cif.gz | 87.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3a3b.ent.gz | 64.9 KB | Display | PDB format |
PDBx/mmJSON format | 3a3b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a3/3a3b ftp://data.pdbj.org/pub/pdb/validation_reports/a3/3a3b | HTTPS FTP |
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-Related structure data
Related structure data | 3a35C 3a3gC 3ddyS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 20911.635 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Photobacterium kishitanii (bacteria) / Gene: luminous bacteria / Plasmid: pET23a / Production host: Escherichia coli (E. coli) / References: UniProt: C4TPG1 #2: Chemical | ChemComp-FMN / | #3: Chemical | ChemComp-RBF / | #4: Water | ChemComp-HOH / | Sequence details | THE EXTERNAL REGION OF LUMP GENE FROM P. KISHITANII IS NOT CLEAR, THEREFORE, DEPOSITORS DESIGNED ...THE EXTERNAL REGION OF LUMP GENE FROM P. KISHITANII | |
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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: 2.12 Å3/Da / Density % sol: 42.05 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 20% (w/v) PEG 4000, 0.2M MgCl2, 100mM Tris-HCl pH8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 5, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→33.22 Å / Num. obs: 22183 / % possible obs: 99.0687 % |
-Processing
Software | Name: REFMAC / Version: 5.2.0019 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3DDY Resolution: 2→33.22 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.914 / SU B: 4.328 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.193 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.7 Å2
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Refinement step | Cycle: LAST / Resolution: 2→33.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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