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Open data
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Basic information
Entry | Database: PDB / ID: 6jt8 | ||||||
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Title | Crystal structure of 450-451_deletion mutant of FGAM Synthetase | ||||||
![]() | Phosphoribosylformylglycinamidine synthase | ||||||
![]() | BIOSYNTHETIC PROTEIN / FGAM Synthetase | ||||||
Function / homology | ![]() phosphoribosylformylglycinamidine synthase / phosphoribosylformylglycinamidine synthase activity / purine nucleotide biosynthetic process / 'de novo' IMP biosynthetic process / glutamine metabolic process / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Sharma, N. / Ahalawat, N. / Sandhu, P. / Mondal, J. / Anand, R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Role of allosteric switches and adaptor domains in long-distance cross-talk and transient tunnel formation. Authors: Sharma, N. / Ahalawat, N. / Sandhu, P. / Strauss, E. / Mondal, J. / Anand, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 318.3 KB | Display | ![]() |
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PDB format | ![]() | 244.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 871 KB | Display | ![]() |
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Full document | ![]() | 895.5 KB | Display | |
Data in XML | ![]() | 63.4 KB | Display | |
Data in CIF | ![]() | 98.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6jt7C ![]() 6jt9C ![]() 6jtaC ![]() 1t3tS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 142452.312 Da / Num. of mol.: 1 / Mutation: G450, G451 deletion mutant Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A0A0D6F9Y3, UniProt: P74881*PLUS, phosphoribosylformylglycinamidine synthase |
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-Non-polymers , 6 types, 1408 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-ADP / | #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-GOL / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.37 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 2M Ammonium Sulphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 14, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 136288 / % possible obs: 100 % / Redundancy: 9.3 % / Rpim(I) all: 0.035 / Net I/σ(I): 27.06 |
Reflection shell | Resolution: 1.9→1.93 Å / Num. unique obs: 6802 / Rpim(I) all: 0.172 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1T3T Resolution: 1.9→48.17 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.965 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.093 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.637 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→48.17 Å
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Refine LS restraints |
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