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Yorodumi- PDB-2b99: Crystal Structure of an archaeal pentameric riboflavin synthase C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2b99 | ||||||
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Title | Crystal Structure of an archaeal pentameric riboflavin synthase Complex with a Substrate analog inhibitor | ||||||
Components | Riboflavin synthase | ||||||
Keywords | TRANSFERASE / lumazine riboflavin | ||||||
Function / homology | Function and homology information riboflavin synthase / riboflavin synthase activity / riboflavin synthase complex / riboflavin biosynthetic process Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.22 Å | ||||||
Authors | Ramsperger, A. / Augustin, M. / Schott, A.K. / Gerhardt, S. / Krojer, T. / Eisenreich, W. / Illarionov, B. / Cushman, M. / Bacher, A. / Huber, R. / Fischer, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Crystal Structure of an Archaeal Pentameric Riboflavin Synthase in Complex with a Substrate Analog Inhibitor: stereochemical implications Authors: Ramsperger, A. / Augustin, M. / Schott, A.K. / Gerhardt, S. / Krojer, T. / Eisenreich, W. / Illarionov, B. / Cushman, M. / Bacher, A. / Huber, R. / Fischer, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2b99.cif.gz | 161.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2b99.ent.gz | 128.2 KB | Display | PDB format |
PDBx/mmJSON format | 2b99.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b9/2b99 ftp://data.pdbj.org/pub/pdb/validation_reports/b9/2b99 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a pentamer. |
-Components
#1: Protein | Mass: 17524.590 Da / Num. of mol.: 5 / Fragment: riboflavin synthase Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Gene: ribC / Plasmid: pNCO113 / Production host: Escherichia coli (E. coli) / References: UniProt: Q58584, riboflavin synthase #2: Chemical | ChemComp-RDL / #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: 2.23 Å3/Da / Density % sol: 44.96 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1 M HEPES, pH 7.0, and 40% MPD., VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 24, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. obs: 34797 / Biso Wilson estimate: 26.3 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→19.92 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 958644.59 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 75.3065 Å2 / ksol: 0.32196 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.22→19.92 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.22→2.36 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Xplor file |
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