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Yorodumi- PDB-4fxu: Crystallographic structure of trimeric riboflavin synthase from B... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fxu | ||||||
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Title | Crystallographic structure of trimeric riboflavin synthase from Brucella abortus | ||||||
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 / : Function and homology information | ||||||
Biological species | Brucella abortus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 | 4fxu.cif.gz | 118.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fxu.ent.gz | 91.4 KB | Display | PDB format |
PDBx/mmJSON format | 4fxu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4fxu_validation.pdf.gz | 447.2 KB | Display | wwPDB validaton report |
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Full document | 4fxu_full_validation.pdf.gz | 454.5 KB | Display | |
Data in XML | 4fxu_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | 4fxu_validation.cif.gz | 30.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fx/4fxu ftp://data.pdbj.org/pub/pdb/validation_reports/fx/4fxu | HTTPS FTP |
-Related structure data
Related structure data | 4e0fSC 4g6iC 4gqnC S: Starting model for refinement C: citing same article (ref.) |
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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: 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: 2.33 Å3/Da / Density % sol: 47.13 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 12% PEG 8000, 10% GLYCEROL, 0.5M 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: 1.9→50 Å / Num. all: 52161 / Num. obs: 52161 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 43.05 Å2 / Rmerge(I) obs: 0.043 / Rsym value: 0.043 / Net I/σ(I): 21.57 |
Reflection shell | Resolution: 1.9→2.01 Å / Redundancy: 7.26 % / Rmerge(I) obs: 0.902 / Mean I/σ(I) obs: 2.02 / Num. unique all: 8216 / Rsym value: 0.902 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB 4E0F Resolution: 1.9→27.72 Å / Cor.coef. Fo:Fc: 0.9396 / Cor.coef. Fo:Fc free: 0.9215 / SU R Cruickshank DPI: 0.154 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 50.38 Å2
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Refine analyze | Luzzati coordinate error obs: 0.294 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→27.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.95 Å / Total num. of bins used: 20
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