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Yorodumi- PDB-2c9b: Lumazine Synthase from Mycobacterium tuberculosus Bound to 3-(1,3... -
+Open data
-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 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 / 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: 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 | 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 (ref.) |
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Similar structure data |
-Links
-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.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Plasmid: PNCO-MT-LS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): XL1-BLUE 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 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting 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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