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Yorodumi- PDB-4g5y: Crystal Structure of Mycobacterium tuberculosis Pantothenate synt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4g5y | ||||||
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Title | Crystal Structure of Mycobacterium tuberculosis Pantothenate synthetase in a ternary complex with ATP and N,N-DIMETHYLTHIOPHENE-3-SULFONAMIDE | ||||||
Components | Pantothenate synthetase | ||||||
Keywords | ligase/ligase inhibitor / drug design / fragment-based / ligase / pantothenate biosynthesis / ligase-ligase inhibitor complex | ||||||
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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Ciulli, A. / Silvestre, H.L. / Blundell, T.L. / Abell, C. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Integrated biophysical approach to fragment screening and validation for fragment-based lead discovery. Authors: Silvestre, H.L. / Blundell, T.L. / Abell, C. / Ciulli, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4g5y.cif.gz | 132.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4g5y.ent.gz | 101.1 KB | Display | PDB format |
PDBx/mmJSON format | 4g5y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4g5y_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 4g5y_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 4g5y_validation.xml.gz | 29.6 KB | Display | |
Data in CIF | 4g5y_validation.cif.gz | 41.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g5/4g5y ftp://data.pdbj.org/pub/pdb/validation_reports/g5/4g5y | HTTPS FTP |
-Related structure data
Related structure data | 4ddhC 4ddkC 4ddmC 4de5C 4ef6C 4efkC 4fzjC 4g5fC 3covS 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#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: MT3707, MTCY07H7B.20, panC, Rv3602c / 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) |
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-Non-polymers , 6 types, 417 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-EOH / #7: 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: 43.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 11-14% w/v PEG3000, 100 150 mM Li2SO4, 100 mM imidazole, pH 8.0, 2-4% v/v ethanol, 10% v/v glycerol and 20 mM MgCl2., 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: 0.97883 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 1, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97883 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→40.28 Å / Num. all: 50957 / Num. obs: 50752 / % possible obs: 99.6 % / Redundancy: 4.112 % / Biso Wilson estimate: 31.163 Å2 / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 15.28 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 4.09 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 3.5 / Num. unique all: 8184 / Rsym value: 0.372 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3COV Resolution: 1.8→37.57 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.656 / SU ML: 0.083 Isotropic thermal model: individual isotropic temperature factors Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 31.563 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→37.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.795→1.842 Å / Total num. of bins used: 20
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