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- PDB-3ime: Crystal Structure of Mycobacterium Tuberculosis Pantothenate Synt... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ime | ||||||
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Title | Crystal Structure of Mycobacterium Tuberculosis Pantothenate Synthetase at 2.40 Ang resolution in complex with fragment compound 1-Benzofuran-2-carboxylic acid | ||||||
![]() | Pantothenate synthetase | ||||||
![]() | LIGASE / Mycobacterium tuberculosis / pantothenate biosynthesis / enzymes / drug design / fragment-based / ATP-binding / Magnesium / Metal-binding / Nucleotide-binding | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ciulli, A. / Hung, A.W. / Silvestre, H.L. / Wen, S. / Blundell, T.L. / Abell, C. | ||||||
![]() | ![]() Title: Application of fragment growing and fragment linking to the discovery of inhibitors of Mycobacterium tuberculosis pantothenate synthetase. Authors: Hung, A.W. / Silvestre, H.L. / Wen, S. / Ciulli, A. / Blundell, T.L. / Abell, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 120.6 KB | Display | ![]() |
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PDB format | ![]() | 93.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 475.4 KB | Display | ![]() |
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Full document | ![]() | 483.1 KB | Display | |
Data in XML | ![]() | 24.8 KB | Display | |
Data in CIF | ![]() | 35.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3imcC ![]() 3imgC ![]() 3isjC ![]() 3iubC ![]() 3iueC ![]() 3ivcC ![]() 3ivgC ![]() 3ivxC ![]() 3covS 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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Components
#1: Protein | Mass: 31571.178 Da / Num. of mol.: 2 / Fragment: UNP residues 1-300 / Mutation: T2A, E77G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P0A5R0, UniProt: P9WIL5*PLUS, pantoate-beta-alanine ligase (AMP-forming) #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.68 % |
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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 lithium sulfate, 100 mM imidazole, pH 8.0, 2-4% v/v ethanol, 10% v/v glycerol and 20 mM magnesium chloride. , VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 21, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.117 Å / Relative weight: 1 |
Reflection | Resolution: 2.39→50 Å / Num. all: 21939 / Num. obs: 21873 / % possible obs: 99.7 % / Redundancy: 3.3 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.127 / Rsym value: 0.127 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2.39→2.46 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.458 / Num. unique all: 1447 / Rsym value: 0.458 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3COV Resolution: 2.39→27.86 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.896 / SU B: 8.61 / SU ML: 0.202 Isotropic thermal model: individual isotropic temperature factors Cross valid method: THROUGHOUT / ESU R: 0.443 / ESU R Free: 0.293 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.708 Å2
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Refinement step | Cycle: LAST / Resolution: 2.39→27.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.39→2.453 Å / Total num. of bins used: 20
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