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Yorodumi- PDB-4mq6: Pantothenate synthase in complex with 2-(5-methoxy-2-(tosylcarbam... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4mq6 | ||||||
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Title | Pantothenate synthase in complex with 2-(5-methoxy-2-(tosylcarbamoyl)-1H-indol-1-yl)acetic acid | ||||||
Components | Pantothenate synthetase | ||||||
Keywords | Ligase/Ligase inhibitor / Alpha Beta 3-Layer(aba) Sandwich Rossmann fold / Pantoate-ligase / ATP binding / Ligase / 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 / SAD / Resolution: 1.7 Å | ||||||
Authors | Silvestre, H.L. / Blundell, T.L. | ||||||
Citation | Journal: Chemmedchem / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mq6.cif.gz | 131.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mq6.ent.gz | 102.3 KB | Display | PDB format |
PDBx/mmJSON format | 4mq6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4mq6_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 4mq6_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 4mq6_validation.xml.gz | 30.3 KB | Display | |
Data in CIF | 4mq6_validation.cif.gz | 43.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mq/4mq6 ftp://data.pdbj.org/pub/pdb/validation_reports/mq/4mq6 | HTTPS FTP |
-Related structure data
Related structure data | 4mueC 4mufC 4mugC 4muhC 4muiC 4mujC 4mukC 4mulC 4munC 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
#1: Protein | Mass: 32609.338 Da / Num. of mol.: 2 / Mutation: T2A, E77G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Production host: Escherichia coli (E. coli) 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42.1 % |
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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: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.97 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→25 Å / Num. all: 223154 / Num. obs: 60099 / % possible obs: 99.9 % / Redundancy: 20.97 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.581 / Mean I/σ(I) obs: 1.9 / Num. unique all: 31738 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.7→25 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.338 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.107 / 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: 25.591 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→25 Å
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Refine LS restraints |
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