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Yorodumi- PDB-2c92: LUMAZINE SYNTHASE FROM MYCOBACTERIUM TUBERCULOSIS BOUND TO 3-(1,3... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2c92 | ||||||
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Title | LUMAZINE SYNTHASE FROM MYCOBACTERIUM TUBERCULOSIS BOUND TO 3-(1,3,7- TRIHYDRO-9-D-RIBITYL-2,6,8-PURINETRIONE-7-YL) PENTANE 1 PHOSPHATE | ||||||
Components | 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASELumazine synthase | ||||||
Keywords | TRANSFERASE / RIBOFLAVIN BIOSYNTHESIS / MYCOBACTERIUM TUBERCULOSIS / LUMAZINE SYNTHASE / INHIBITOR BINDING | ||||||
Function / homology | Function and homology information 6,7-dimethyl-8-ribityllumazine synthase / 6,7-dimethyl-8-ribityllumazine synthase activity / riboflavin synthase complex / riboflavin biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Morgunova, E. / Illarionov, B. / Jin, G. / Haase, I. / Fischer, M. / Cushman, M. / Bacher, A. / Ladenstein, R. | ||||||
Citation | Journal: FEBS J. / Year: 2006 Title: Structural and Thermodynamic Insights Into the Binding Mode of Five Novel Inhibitors of Lumazine Synthase from Mycobacterium Tuberculosis. Authors: Morgunova, E. / Illarionov, B. / Sambaiah, T. / Haase, I. / Bacher, A. / Cushman, M. / Fischer, M. / Ladenstein, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2c92.cif.gz | 167.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c92.ent.gz | 130.8 KB | Display | PDB format |
PDBx/mmJSON format | 2c92.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c9/2c92 ftp://data.pdbj.org/pub/pdb/validation_reports/c9/2c92 | HTTPS FTP |
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-Related structure data
Related structure data | 2c94C 2c97C 2c9bC 2c9dC 1w19S 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 on special symmetry positions |
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-Components
-Protein , 1 types, 5 molecules ABCDE
#1: Protein | Mass: 16387.559 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Plasmid: PNCO-MT-LS / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): XL1-BLUE References: UniProt: P66034, UniProt: P9WHE9*PLUS, riboflavin synthase |
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-Non-polymers , 5 types, 688 molecules
#2: Chemical | ChemComp-TP6 / #3: Chemical | ChemComp-K / #4: Chemical | #5: Chemical | ChemComp-MPD / ( | #6: 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: 2.5 Å3/Da / Density % sol: 48 % |
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Crystal grow | pH: 6.41 / Details: pH 6.41 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.092 |
Detector | Type: MARRESEACH / Detector: IMAGE PLATE / Date: Jun 26, 2004 / Details: CYLINDRICAL MIRROR |
Radiation | Monochromator: SI(111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.092 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 103691 / % possible obs: 85.8 % / Observed criterion σ(I): 1 / Redundancy: 2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 1.6→1.64 Å / Redundancy: 2 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.37 / % possible all: 80.3 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1W19 Resolution: 1.6→10 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.719 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-13 ARE DISORDERED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.87 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→10 Å
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Refine LS restraints |
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