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Yorodumi- PDB-1w19: Lumazine Synthase from Mycobacterium tuberculosis bound to 3-(1,3... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1w19 | ||||||
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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)propane 1-phosphate | ||||||
Components | 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE | ||||||
Keywords | TRANSFERASE / RIBOFLAVIN BIOSYNTHESIS / 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: 2 Å | ||||||
Authors | Morgunova, E. / Meining, W. / Illarionov, B. / Haase, I. / Fischer, M. / Cushman, M. / Bacher, A. / Ladenstein, R. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Crystal Structure of Lumazine Synthase from Mycobacterium Tuberculosis as a Target for Rational Drug Design: Binding Mode of a New Class of Purinetrione Inhibitors(,) Authors: Morgunova, E. / Meining, W. / Illarionov, B. / Haase, I. / Jin, G. / 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 | 1w19.cif.gz | 171.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w19.ent.gz | 134.2 KB | Display | PDB format |
PDBx/mmJSON format | 1w19.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1w19_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 1w19_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 1w19_validation.xml.gz | 41.1 KB | Display | |
Data in CIF | 1w19_validation.cif.gz | 55.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w1/1w19 ftp://data.pdbj.org/pub/pdb/validation_reports/w1/1w19 | HTTPS FTP |
-Related structure data
Related structure data | 1w29C 1ejbS 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: P71685, UniProt: P9WHE9*PLUS, riboflavin synthase |
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-Non-polymers , 10 types, 660 molecules
#2: Chemical | ChemComp-ACY / #3: Chemical | #4: Chemical | ChemComp-T1P / | #5: Chemical | ChemComp-K / #6: Chemical | ChemComp-T2P / | #7: Chemical | #8: Chemical | ChemComp-T5P / | #9: Chemical | #10: Chemical | ChemComp-D1D / ( | #11: 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: 2.4 Å3/Da / Density % sol: 48 % |
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Crystal grow | pH: 7 Details: ADA BUFFER PH 6.4, 3.5M POTASSIUM ACETATE,0.5 M DTT,10%MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.85 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 6, 2003 / Details: MIRRORS |
Radiation | Monochromator: TRIANGULAR MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.85 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 52169 / % possible obs: 99.4 % / Observed criterion σ(I): 1 / Redundancy: 2.08 % / Biso Wilson estimate: 20.8 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.26 |
Reflection shell | Resolution: 2→2.02 Å / Redundancy: 1 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 3.38 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EJB Resolution: 2→19.54 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.522 / SU ML: 0.097 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.25 Å2
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Refinement step | Cycle: LAST / Resolution: 2→19.54 Å
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Refine LS restraints |
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