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Yorodumi- PDB-3a3g: Crystal structure of LumP complexed with 6,7-dimethyl-8-(1'-D-rib... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3a3g | ||||||
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Title | Crystal structure of LumP complexed with 6,7-dimethyl-8-(1'-D-ribityl) lumazine | ||||||
Components | Lumazine protein | ||||||
Keywords | LUMINESCENT PROTEIN / luminous bacteria / lumazine protein / photobacterium | ||||||
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 | 3a3g.cif.gz | 86.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3a3g.ent.gz | 65.2 KB | Display | PDB format |
PDBx/mmJSON format | 3a3g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3a3g_validation.pdf.gz | 984 KB | Display | wwPDB validaton report |
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Full document | 3a3g_full_validation.pdf.gz | 993.2 KB | Display | |
Data in XML | 3a3g_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | 3a3g_validation.cif.gz | 25.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a3/3a3g ftp://data.pdbj.org/pub/pdb/validation_reports/a3/3a3g | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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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 | #3: 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 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.45 % |
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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-NE3A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 28, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→44.766 Å / Num. obs: 23305 / % possible obs: 99.7563 % |
-Processing
Software | Name: REFMAC / Version: 5.2.0019 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→44.766 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.886 / SU B: 4.062 / SU ML: 0.116 / Isotropic thermal model: PDB ENTRY 3DDY / Cross valid method: THROUGHOUT / ESU R: 0.203 / ESU R Free: 0.186 / 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: 19.594 Å2
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Refinement step | Cycle: LAST / Resolution: 2→44.766 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.001→2.053 Å / Total num. of bins used: 20
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