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Yorodumi- PDB-6qmi: Phosphopantetheine adenylyltransferase from Mycobacterium tubercu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qmi | |||||||||
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Title | Phosphopantetheine adenylyltransferase from Mycobacterium tuberculosis in complex with 3-(1H-indol-1-yl)propanoic acid at 1.7A resolution. | |||||||||
Components | Phosphopantetheine adenylyltransferase | |||||||||
Keywords | TRANSFERASE / CoaD / PPAT / Complex | |||||||||
Function / homology | Function and homology information pantetheine-phosphate adenylyltransferase / pantetheine-phosphate adenylyltransferase activity / protein hexamerization / coenzyme A biosynthetic process / ATP binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.781 Å | |||||||||
Authors | Blaszczyk, M. / Blundell, T.L. | |||||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Fragment linking applied to the discovery of Mycobacterium tuberculosis phosphopantetheine adenylyltransferase inhibitors Authors: Blaszczyk, M. / El Bakali, J. / Boland, J.A. / Spry, C. / Dias, M. / Blundell, T.L. / Abel, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qmi.cif.gz | 44.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qmi.ent.gz | 29.9 KB | Display | PDB format |
PDBx/mmJSON format | 6qmi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qm/6qmi ftp://data.pdbj.org/pub/pdb/validation_reports/qm/6qmi | HTTPS FTP |
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-Related structure data
Related structure data | 6g6vC 6qmfC 6qmgC 6qmhC 1tfuS 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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 17792.385 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: coaD, kdtB, Rv2965c, MTCY349.22, u0002e / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P9WPA5, pantetheine-phosphate adenylyltransferase |
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#2: Chemical | ChemComp-9FH / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.43 % / Description: cubes |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: MPD, CoHexamine Chloride, Cacodylate/Tris / PH range: 6.5-8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.95 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 23, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.781→34.032 Å / Num. obs: 20290 / % possible obs: 99.9 % / Redundancy: 8.3 % / Biso Wilson estimate: 34.42 Å2 / Rpim(I) all: 0.012 / Rrim(I) all: 0.036 / Rsym value: 0.031 / Net I/av σ(I): 13.6 / Net I/σ(I): 33 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1TFU Resolution: 1.781→34.032 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.34
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 87.87 Å2 / Biso mean: 41.1592 Å2 / Biso min: 20.63 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.781→34.032 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7
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