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- PDB-6m2t: The crystal structure of benzoate coenzyme A ligase double mutant... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6m2t | |||||||||
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Title | The crystal structure of benzoate coenzyme A ligase double mutant (H333A/I334A) in complex with 2-methyl-thiazole-5 carboxylate-AMP | |||||||||
![]() | Benzoate-coenzyme A ligase | |||||||||
![]() | LIGASE | |||||||||
Function / homology | ![]() acid-thiol ligase activity / CoA-ligase activity / secondary metabolite biosynthetic process / ATP binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Li, T.L. / Adhikari, K. | |||||||||
![]() | ![]() Title: The crystal structure of benzoate coenzyme A ligase double mutant (H333A/I334A) in complex with 2-methyl-thiazole-5 carboxylate-AMP Authors: Li, T.L. / Adhikari, K. / Malek, Z.S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 425.4 KB | Display | ![]() |
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PDB format | ![]() | 341.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.5 MB | Display | ![]() |
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Full document | ![]() | 2.6 MB | Display | |
Data in XML | ![]() | 86.3 KB | Display | |
Data in CIF | ![]() | 125.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6m20S S: Starting model for refinement |
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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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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 56683.098 Da / Num. of mol.: 4 / Mutation: T83A, H333A, I334A, G341D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: badA / Production host: ![]() #2: Chemical | ChemComp-AMP / #3: Chemical | ChemComp-6V9 / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.05 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 4000, 0.1 M sodium chloride, 0.2 M MES |
-Data collection
Diffraction | Mean temperature: 200 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Jun 19, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.138→27.783 Å / Num. obs: 113090 / % possible obs: 99.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 25.33 |
Reflection shell | Resolution: 2.14→2.22 Å / Rmerge(I) obs: 0.2 / Num. unique obs: 113090 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6M20 Resolution: 2.14→27.78 Å / SU ML: 0.19 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 20.42 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.14→27.78 Å
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Refine LS restraints |
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LS refinement shell |
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