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Yorodumi- PDB-3cov: Crystal Structure of Mycobacterium Tuberculosis Pantothenate Synt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cov | ||||||
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Title | Crystal Structure of Mycobacterium Tuberculosis Pantothenate Synthetase at 1.5 Ang resolution- apo form | ||||||
Components | Pantothenate synthetase | ||||||
Keywords | LIGASE / Mycobacterium tuberculosis / pantothenate biosynthesis / enzymes / drug design / ATP-binding / Magnesium / Metal-binding / Nucleotide-binding | ||||||
Function / homology | Function and homology information beta-alanine metabolic process / pantoate-beta-alanine ligase (AMP-forming) / pantoate-beta-alanine ligase activity / pantothenate biosynthetic process / manganese ion binding / magnesium ion binding / ATP binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Ciulli, A. / Chirgadze, D.Y. / Blundell, T.L. / Abell, C. | ||||||
Citation | Journal: Chembiochem / Year: 2008 Title: Inhibition of Mycobacterium tuberculosis pantothenate synthetase by analogues of the reaction intermediate. Authors: Ciulli, A. / Scott, D.E. / Ando, M. / Reyes, F. / Saldanha, S.A. / Tuck, K.L. / Chirgadze, D.Y. / Blundell, T.L. / Abell, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cov.cif.gz | 131.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cov.ent.gz | 101.2 KB | Display | PDB format |
PDBx/mmJSON format | 3cov.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/co/3cov ftp://data.pdbj.org/pub/pdb/validation_reports/co/3cov | HTTPS FTP |
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-Related structure data
Related structure data | 3cowC 3coyC 3cozC 1mopS 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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Details | The biological assembly is a dimer contained in the asymmetric unit. |
-Components
#1: Protein | Mass: 31571.178 Da / Num. of mol.: 2 / Mutation: T2A, E77G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: panC / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) References: UniProt: P0A5R0, UniProt: P9WIL5*PLUS, pantoate-beta-alanine ligase (AMP-forming) #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-EOH / #5: 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: 2.19 Å3/Da / Density % sol: 43.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 12-14% PEG3000, 100-150 mM Li2SO4, 100 mM imidazole, 2-4% v/v ethanol, 5-10% v/v glycerol and 20 mM MgCl2., pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.973 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 26, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.973 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. all: 86748 / Num. obs: 86488 / % possible obs: 99.7 % / Observed criterion σ(I): 2.5 / Redundancy: 3.7 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.341 / Num. unique all: 5725 / Rsym value: 0.341 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1MOP Resolution: 1.5→47.67 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.174 / SU ML: 0.045 Isotropic thermal model: individual isotropic temperature factors Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.073 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.743 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→47.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.501→1.54 Å / Total num. of bins used: 20
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