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- PDB-4muh: Crystal structure of pantothenate synthetase in complex with 2-(2... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4muh | ||||||
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Title | Crystal structure of pantothenate synthetase in complex with 2-(2-(5-acetamido-1,3,4-thiadiazol-2-ylsulfonylcarbamoyl)-5-methoxy-1H-indol-1-yl)acetic acid | ||||||
![]() | Pantothenate synthetase | ||||||
![]() | ligase/ligase inhibitor / Alpha Beta 3-Layer(aba) Sandwich Rossmann fold / Pantoate-ligase / ATP binding / ligase-ligase inhibitor complex | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Silvestre, H.L. / Blundell, T.L. | ||||||
![]() | ![]() Title: Optimization of Inhibitors of Mycobacterium tuberculosis Pantothenate Synthetase Based on Group Efficiency Analysis. Authors: Hung, A.W. / Silvestre, H.L. / Wen, S. / George, G.P. / Boland, J. / Blundell, T.L. / Ciulli, A. / 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 | ![]() | 129.5 KB | Display | ![]() |
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PDB format | ![]() | 101 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 28.4 KB | Display | |
Data in CIF | ![]() | 40.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4mq6C ![]() 4mueC ![]() 4mufC ![]() 4mugC ![]() 4muiC ![]() 4mujC ![]() 4mukC ![]() 4mulC ![]() 4munC ![]() 3le8S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 31500.100 Da / Num. of mol.: 2 / 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 | ChemComp-EOH / #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.15 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 11-14% w/v PEG3000, 150 mM lithium sulfate, 100 mM imidazole, 2% v/v ethanol, 10% v/v glycerol, 20 mM magnesium chloride , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→28.61 Å / Num. all: 210679 / Num. obs: 57664 / % possible obs: 100 % / Redundancy: 3.7 % / Biso Wilson estimate: 20.77 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.72→1.81 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 2 / Num. unique all: 30188 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 3LE8 Resolution: 1.72→28 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.306 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.109 / 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: 23.595 Å2
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Refinement step | Cycle: LAST / Resolution: 1.72→28 Å
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Refine LS restraints |
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