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- PDB-5gtd: o-Succinylbenzoate CoA Synthetase (MenE) from Bacillus Subtilis i... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5gtd | |||||||||
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Title | o-Succinylbenzoate CoA Synthetase (MenE) from Bacillus Subtilis in Complex with the Acyl-adenylate Intermediate OSB-AMP | |||||||||
![]() | 2-succinylbenzoate--CoA ligase | |||||||||
![]() | LIGASE / Adenylate-forming Enzyme / adenylate intermdiate / OSBAMP / in-line backside nucleophilic substitution / strained conformation | |||||||||
Function / homology | ![]() o-succinylbenzoate-CoA ligase / o-succinylbenzoate-CoA ligase activity / CoA-ligase activity / menaquinone biosynthetic process / ATP binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Chen, Y. / Guo, Z. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Mechanistic Insights from the Crystal Structure of Bacillus subtilis o-Succinylbenzoyl-CoA Synthetase Complexed with the Adenylate Intermediate Authors: Chen, Y. / Jiang, Y. / Guo, Z. #1: ![]() Title: Structural Basis for the ATP-dependent Configuration of Adenylation Active Site in Bacillus subtilis o-Succinylbenzoyl-CoA Synthetase. Authors: Chen, Y. / Sun, Y. / Song, H. / Guo, Z. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 349.8 KB | Display | ![]() |
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PDB format | ![]() | 283.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1023.7 KB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 34 KB | Display | |
Data in CIF | ![]() | 45 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5burS 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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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 55269.117 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 168 / Gene: menE, BSU30790 / Production host: ![]() ![]() |
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-Non-polymers , 7 types, 50 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/AMP.gif)
![](data/chem/img/OSB.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/AMP.gif)
![](data/chem/img/OSB.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-PEG / | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-MG / | #7: Chemical | ChemComp-IMD / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.31 Å3/Da / Density % sol: 62.81 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 10% PEG 6000, 10.5% MPD, 0.094M HEPES pH7.3, 0.012M imidazole, 0.12M sodium acetate, 0.6% PEG8000, 0.48% ethylene glycol PH range: 7.0-7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 26, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.69→31.96 Å / Num. obs: 39783 / % possible obs: 99.17 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.083 / Rsym value: 0.089 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 2.69→2.79 Å / Rmerge(I) obs: 0.738 / Mean I/σ(I) obs: 3.2 / CC1/2: 0.868 / % possible all: 98.75 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5BUR Resolution: 2.69→31.96 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.46 / 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: 2.69→31.96 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 51.9746 Å / Origin y: -143.5064 Å / Origin z: 0.978 Å
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Refinement TLS group | Selection details: all |