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- PDB-6yvq: Crystal structure of SAICAR Synthetase (PurC) from Mycobacterium ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6yvq | |||||||||
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Title | Crystal structure of SAICAR Synthetase (PurC) from Mycobacterium abscessus in apo form | |||||||||
![]() | Phosphoribosylaminoimidazole-succinocarboxamide synthase | |||||||||
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Function / homology | ![]() ![]() ![]() ![]() 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 | ![]() | 134.7 KB | Display | ![]() |
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PDB format | ![]() | 103.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6yx3C ![]() 6yy6C ![]() 6yy7C ![]() 6yy8C ![]() 6yy9C ![]() 6yyaC ![]() 6yybC ![]() 6yycC ![]() 6yydC ![]() 6z0qC ![]() 6z0rC ![]() 3r9rS 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.) ![]() ![]() Strain: ATCC 19977 / DSM 44196 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543 Gene: purC, MAB_0689 / Production host: ![]() ![]() ![]() References: UniProt: B1MHW4, ![]() | ||||||
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#2: Chemical | ![]() #3: Chemical | ![]() #4: Water | ChemComp-HOH / | ![]() Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.99 % |
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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 5.5, 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![]() | ||||||||||||||||||||||||
Reflection | Resolution: 1.48→45.02 Å / Num. obs: 41027 / % possible obs: 89.7 % / Redundancy: 4.1 % / Biso Wilson estimate: 16.49 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.04 / Rrim(I) all: 0.085 / Net I/σ(I): 10.8 | ||||||||||||||||||||||||
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: 3R9R Resolution: 1.48→45.018 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.43 / Phase error: 21.66
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 92.85 Å2 / Biso mean: 22.7098 Å2 / Biso min: 10.7 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.48→45.018 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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