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Yorodumi- PDB-4g6i: Crystallographic structure of trimeric riboflavin synthase from B... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4g6i | ||||||
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Title | Crystallographic structure of trimeric riboflavin synthase from Brucella abortus in complex with roseoflavin | ||||||
Components | Riboflavin synthase subunit alpha | ||||||
Keywords | TRANSFERASE / beta barrel / alpha + beta protein / riboflavin biosynthesis | ||||||
Function / homology | Elongation Factor Tu (Ef-tu); domain 3 - #20 / Elongation Factor Tu (Ef-tu); domain 3 / Beta Barrel / Mainly Beta / Chem-RS3 / : Function and homology information | ||||||
Biological species | Brucella abortus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å | ||||||
Authors | Serer, M.I. / Bonomi, H.R. / Guimaraes, B.G. / Rossi, R.C. / Goldbaum, F.A. / Klinke, S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Crystallographic and kinetic study of riboflavin synthase from Brucella abortus, a chemotherapeutic target with an enhanced intrinsic flexibility. Authors: Serer, M.I. / Bonomi, H.R. / Guimaraes, B.G. / Rossi, R.C. / Goldbaum, F.A. / Klinke, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4g6i.cif.gz | 132.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4g6i.ent.gz | 103.2 KB | Display | PDB format |
PDBx/mmJSON format | 4g6i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4g6i_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 4g6i_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 4g6i_validation.xml.gz | 26.2 KB | Display | |
Data in CIF | 4g6i_validation.cif.gz | 35.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g6/4g6i ftp://data.pdbj.org/pub/pdb/validation_reports/g6/4g6i | HTTPS FTP |
-Related structure data
Related structure data | 4e0fSC 4fxuC 4gqnC 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
#1: Protein | Mass: 23320.361 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brucella abortus (bacteria) / Gene: RIBE / Plasmid: PET22B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: G8SX20, riboflavin synthase #2: Chemical | ChemComp-RS3 / #3: 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: 2.31 Å3/Da / Density % sol: 46.72 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 12% PEG 8000, 10% GLYCEROL, 0.5 M POTASSIUM CHLORIDE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: May 13, 2012 / Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS |
Radiation | Monochromator: CHANNEL CUT CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98011 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→50 Å / Num. all: 60197 / Num. obs: 60197 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.96 % / Biso Wilson estimate: 34.63 Å2 / Rmerge(I) obs: 0.026 / Rsym value: 0.026 / Net I/σ(I): 21.24 |
Reflection shell | Resolution: 1.78→1.89 Å / Redundancy: 2.97 % / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 2.1 / Num. unique all: 9547 / Rsym value: 0.514 / % possible all: 95.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB 4E0F Resolution: 1.78→32.29 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.824 / SU ML: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.159 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: 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: 34.964 Å2
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Refinement step | Cycle: LAST / Resolution: 1.78→32.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.781→1.827 Å / Total num. of bins used: 20
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