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Yorodumi- PDB-5buq: Unliganded Form of O-succinylbenzoate Coenzyme A Synthetase (MenE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5buq | ||||||
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Title | Unliganded Form of O-succinylbenzoate Coenzyme A Synthetase (MenE) from Bacillus Subtilis, Solved at 1.98 Angstroms | ||||||
Components | 2-succinylbenzoate--CoA ligase | ||||||
Keywords | LIGASE / apo / ATP / AMP / enzyme mechanism / protein conformation / vitamin K2 / adenylate forming enzyme / domain alteration / open-closed conformational change | ||||||
Function / homology | Function and homology information o-succinylbenzoate-CoA ligase / o-succinylbenzoate-CoA ligase activity / CoA-ligase activity / menaquinone biosynthetic process / ATP binding Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å | ||||||
Authors | Chen, Y. / Sun, Y. / Song, H. / Guo, Z. | ||||||
Funding support | Hong Kong, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5buq.cif.gz | 382 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5buq.ent.gz | 304.9 KB | Display | PDB format |
PDBx/mmJSON format | 5buq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5buq_validation.pdf.gz | 453.9 KB | Display | wwPDB validaton report |
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Full document | 5buq_full_validation.pdf.gz | 462.1 KB | Display | |
Data in XML | 5buq_validation.xml.gz | 44.5 KB | Display | |
Data in CIF | 5buq_validation.cif.gz | 67.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bu/5buq ftp://data.pdbj.org/pub/pdb/validation_reports/bu/5buq | HTTPS FTP |
-Related structure data
Related structure data | 5burC 5busC 3iplS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 55269.117 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Strain: 168 / Gene: menE, BSU30790 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P23971, o-succinylbenzoate-CoA ligase #2: Chemical | ChemComp-ACT / | #3: Chemical | ChemComp-CA / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.15 Details: 8.1% (w/v) PEG8000, 0.09M cacodylate/HCl pH 6.15, 0.144M calcium acetate, 12.6% glycerol with additive agent of 0.049M sodium phosphate monobasic and 0.091M Potassium phosphate dibasic |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.973 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 3, 2014 |
Radiation | Monochromator: double / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.973 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→33.27 Å / Num. obs: 73620 / % possible obs: 98.83 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.04759 / Rsym value: 0.0673 / Net I/σ(I): 22.06 |
Reflection shell | Resolution: 1.98→2.051 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.2043 / Mean I/σ(I) obs: 9.05 / % possible all: 99.15 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3IPL(N-domain of S. aureus MenE), chainA Resolution: 1.98→33.27 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.87 / 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: 1.98→33.27 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: 82.8803 Å / Origin y: -76.1611 Å / Origin z: 112.9226 Å
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Refinement TLS group | Selection details: all |