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- PDB-2a86: Crystal structure of A Pantothenate synthetase complexed with AMP... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2a86 | ||||||
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Title | Crystal structure of A Pantothenate synthetase complexed with AMP and beta-alanine | ||||||
![]() | Pantoate--beta-alanine ligase | ||||||
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Function / homology | ![]() beta-alanine metabolic process / pantoate-beta-alanine ligase (AMP-forming) / ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Wang, S. / Eisenberg, D. / TB Structural Genomics Consortium (TBSGC) | ||||||
![]() | ![]() Title: Crystal Structure of the Pantothenate Synthetase from Mycobacterium tuberculosis, Snapshots of the Enzyme in Action. Authors: Wang, S. / Eisenberg, D. #1: ![]() Title: Crystal structures of a pantothenate synthetase and its complexes with substrates and a reaction intermediate Authors: Wang, S. / Eisenberg, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 126.4 KB | Display | ![]() |
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PDB format | ![]() | 98.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2a7xC ![]() 2a84C ![]() 2a88C ![]() 1mopS C: citing same article ( S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 31500.100 Da / Num. of mol.: 2 / Mutation: T2A, E77G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: P0A5R0, UniProt: P9WIL5*PLUS, pantoate-beta-alanine ligase (AMP-forming) |
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-Non-polymers , 6 types, 328 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/AMP.gif)
![](data/chem/img/BAL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EOH.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/AMP.gif)
![](data/chem/img/BAL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EOH.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SO4 / ![]() | ||||||||
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#3: Chemical | ![]() #4: Chemical | ![]() #5: Chemical | ChemComp-GOL / ![]() #6: Chemical | ChemComp-EOH / ![]() #7: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.4 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 3000, glycerol, ethanol, magnesium chloride, lithium sulfate, imidazole, pH 8.0, vapor diffusion, hanging drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.85→50 Å / Num. all: 45909 / Num. obs: 45909 / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 23.6 |
Reflection shell | Resolution: 1.85→1.9 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.547 / Mean I/σ(I) obs: 2.5 / % possible all: 98.1 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: pdb entry 1MOP Resolution: 1.85→20 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.956 / SU B: 5.159 / SU ML: 0.081 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.451 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.899 Å / Total num. of bins used: 20
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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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