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Yorodumi- PDB-2c9b: Lumazine Synthase from Mycobacterium tuberculosus Bound to 3-(1,3... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 2c9b | ||||||
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| Title | Lumazine Synthase from Mycobacterium tuberculosus Bound to 3-(1,3,7- TRIHYDRO-9-D-RIBITYL-2,6,8-PURINETRIONE-7-YL) | ||||||
Components | 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE | ||||||
Keywords | TRANSFERASE / INHIBITOR BINDING | ||||||
| Function / homology | Function and homology information6,7-dimethyl-8-ribityllumazine synthase / 6,7-dimethyl-8-ribityllumazine synthase activity / riboflavin synthase complex / riboflavin biosynthetic process / cytosol / cytoplasm Similarity search - Function | ||||||
| Biological species | ![]() | ||||||
| Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Morgunova, E. / Illarionov, B. / Jin, G. / Haase, I. / Fischer, M. / Cushman, M. / Bacher, A. / Ladenstein, R. | ||||||
Citation | Journal: FEBS J. / Year: 2006Title: 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. | ||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 2c9b.cif.gz | 271 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb2c9b.ent.gz | 216.7 KB | Display | PDB format |
| PDBx/mmJSON format | 2c9b.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 2c9b_validation.pdf.gz | 3.1 MB | Display | wwPDB validaton report |
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| Full document | 2c9b_full_validation.pdf.gz | 3.1 MB | Display | |
| Data in XML | 2c9b_validation.xml.gz | 57.8 KB | Display | |
| Data in CIF | 2c9b_validation.cif.gz | 78.7 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c9/2c9b ftp://data.pdbj.org/pub/pdb/validation_reports/c9/2c9b | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 2c92C ![]() 2c94C ![]() 2c97C ![]() 2c9dC ![]() 1w19S S: Starting model for refinement C: citing same article ( |
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| Similar structure data |
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Links
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Assembly
| Deposited unit | ![]()
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| Unit cell |
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| Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: PO4 / End label comp-ID: PO4 / Refine code: 2 / Label seq-ID: 15
NCS ensembles :
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Components
-Protein , 1 types, 10 molecules ABCDEFGHIJ
| #1: Protein | Mass: 16387.559 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P66034, UniProt: P9WHE9*PLUS, riboflavin synthase |
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-Non-polymers , 5 types, 691 molecules 








| #2: Chemical | ChemComp-PUG / #3: Chemical | ChemComp-K / #4: Chemical | ChemComp-PO4 / #5: Chemical | #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: 2.36 Å3/Da / Density % sol: 50 % |
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| Crystal grow | pH: 6.4 / Details: pH 6.40 |
-Data collection
| Diffraction | Mean temperature: 105 K |
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| Diffraction source | Source: ROTATING ANODE / Type: ROTATING ANODE / Wavelength: 1.5418 |
| Detector | Type: MARRESEACH / Detector: IMAGE PLATE / Date: May 20, 2005 / Details: MIRRORS |
| Radiation | Monochromator: OSMIC FOCUSING MIRROR SYSTEM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
| Reflection | Resolution: 2.65→15 Å / Num. obs: 59532 / % possible obs: 89.1 % / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 4.4 |
| Reflection shell | Resolution: 2.65→2.71 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.25 / % possible all: 85.7 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting model: PDB ENTRY 1W19 Resolution: 2.75→10 Å / Cor.coef. Fo:Fc: 0.878 / Cor.coef. Fo:Fc free: 0.798 / SU B: 37.743 / SU ML: 0.416 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.536 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Displacement parameters | Biso mean: 32.84 Å2
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| Refinement step | Cycle: LAST / Resolution: 2.75→10 Å
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| Refine LS restraints |
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