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- PDB-6yx3: Crystal structure of SAICAR Synthetase (PurC) from Mycobacterium ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6yx3 | |||||||||
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Title | Crystal structure of SAICAR Synthetase (PurC) from Mycobacterium abscessus in complex with ATP | |||||||||
![]() | Phosphoribosylaminoimidazole-succinocarboxamide synthase | |||||||||
![]() | LIGASE / SAICAR synthetase / Phosphoribosylaminoimidazole-succinocarboxamide synthase / PurC / Purine Biosynthesis | |||||||||
Function / homology | ![]() phosphoribosylaminoimidazolesuccinocarboxamide synthase / phosphoribosylaminoimidazolesuccinocarboxamide synthase activity / 'de novo' IMP biosynthetic process / ATP binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Thomas, S.E. / Charoensutthivarakul, S. / Coyne, A.G. / Abell, C. / Blundell, T.L. | |||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Development of Inhibitors of SAICAR Synthetase (PurC) from Mycobacterium abscessus Using a Fragment-Based Approach. Authors: Charoensutthivarakul, S. / Thomas, S.E. / Curran, A. / Brown, K.P. / Belardinelli, J.M. / Whitehouse, A.J. / Acebron-Garcia-de-Eulate, M. / Sangan, J. / Gramani, S.G. / Jackson, M. / Mendes, ...Authors: Charoensutthivarakul, S. / Thomas, S.E. / Curran, A. / Brown, K.P. / Belardinelli, J.M. / Whitehouse, A.J. / Acebron-Garcia-de-Eulate, M. / Sangan, J. / Gramani, S.G. / Jackson, M. / Mendes, V. / Floto, R.A. / Blundell, T.L. / Coyne, A.G. / 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 | ![]() | 151 KB | Display | ![]() |
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PDB format | ![]() | 114.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 851.6 KB | Display | ![]() |
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Full document | ![]() | 851.8 KB | Display | |
Data in XML | ![]() | 16.5 KB | Display | |
Data in CIF | ![]() | 26.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6yvqSC ![]() 6yy6C ![]() 6yy7C ![]() 6yy8C ![]() 6yy9C ![]() 6yyaC ![]() 6yybC ![]() 6yycC ![]() 6yydC ![]() 6z0qC ![]() 6z0rC 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 33900.176 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: purC, MAB_0689 / Production host: ![]() ![]() References: UniProt: B1MHW4, phosphoribosylaminoimidazolesuccinocarboxamide synthase | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-MG / | #4: Chemical | ChemComp-ATP / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.28 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / Details: 0.2 M LiSO4, 0.1 M Bis-Tris pH 6.0, 25 % PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 7, 2015 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.22→45.61 Å / Num. obs: 62449 / % possible obs: 76.4 % / Redundancy: 4.9 % / Biso Wilson estimate: 9.45 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.021 / Rrim(I) all: 0.049 / Net I/σ(I): 23.1 / Num. measured all: 302987 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Phasing MR | Model details: Phaser MODE: MR_AUTO |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6YVQ Resolution: 1.22→37.165 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 21.23 / Stereochemistry target values: ML
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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 max: 118.28 Å2 / Biso mean: 16.8884 Å2 / Biso min: 5.59 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.22→37.165 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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