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Open data
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Basic information
Entry | Database: PDB / ID: 6u7a | ||||||
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Title | Rv3722c in complex with kynurenine | ||||||
![]() | Aminotransferase | ||||||
![]() | TRANSFERASE / Aminotransferase / Mycobacterium tuberculosis | ||||||
Function / homology | ![]() aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mandyoli, L. / Sacchettini, J. | ||||||
![]() | ![]() Title: Aspartate aminotransferase Rv3722c governs aspartate-dependent nitrogen metabolism in Mycobacterium tuberculosis. Authors: Jansen, R.S. / Mandyoli, L. / Hughes, R. / Wakabayashi, S. / Pinkham, J.T. / Selbach, B. / Guinn, K.M. / Rubin, E.J. / Sacchettini, J.C. / Rhee, K.Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 724.1 KB | Display | ![]() |
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PDB format | ![]() | 546.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 579.2 KB | Display | ![]() |
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Full document | ![]() | 596.1 KB | Display | |
Data in XML | ![]() | 6.2 KB | Display | |
Data in CIF | ![]() | 43.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6u78C ![]() 5c6uS 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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4 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 8 molecules ABCDEFGH
#1: Protein | Mass: 47356.754 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: DKC2_3956, DSI35_31455, ERS007661_01687, ERS007663_01945, ERS007665_01586, ERS007670_01863, ERS007672_01473, ERS007679_00092, ERS007681_00098, ERS007688_00789, ERS007703_00081, ERS007720_02793, ...Gene: DKC2_3956, DSI35_31455, ERS007661_01687, ERS007663_01945, ERS007665_01586, ERS007670_01863, ERS007672_01473, ERS007679_00092, ERS007681_00098, ERS007688_00789, ERS007703_00081, ERS007720_02793, ERS007722_01790, ERS023446_00155, ERS024276_02601, ERS027646_02441, ERS027652_01615, ERS027653_01450, ERS027656_00154, ERS027666_02093, ERS031537_01226, ERS124361_00578, EUB07_12880, EUB11_07270, EUB16_18395, SAMEA2682835_06491, SAMEA2682864_02982, SAMEA2683035_02356 Production host: ![]() ![]() |
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-Non-polymers , 8 types, 1079 molecules ![](data/chem/img/Q0P.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/KYA.gif)
![](data/chem/img/PMP.gif)
![](data/chem/img/PLP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/KYA.gif)
![](data/chem/img/PMP.gif)
![](data/chem/img/PLP.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-Q0P / ( | ||||||||||||
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#3: Chemical | ChemComp-PO4 / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-1PE / #6: Chemical | ChemComp-KYA / #7: Chemical | ChemComp-PMP / #8: Chemical | #9: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.18 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 100 mM sodium phosphate dibasic / citric acid, 40% ethanol, 5% PEG1000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 2, 2019 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.22→48.361 Å / Num. obs: 178462 / % possible obs: 89.5 % / Redundancy: 7.5 % / Biso Wilson estimate: 30.89 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.138 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.223→2.228 Å / Num. unique obs: 7803 / CC1/2: 0.63 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 5C6U Resolution: 2.22→32.46 Å / SU ML: 0.2683 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 24.5626 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.9 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.22→32.46 Å
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Refine LS restraints |
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LS refinement shell |
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