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Yorodumi- PDB-6m2o: Double mutant(H333A/I334A) crystal structure of benzoate coenzyme... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6m2o | ||||||
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Title | Double mutant(H333A/I334A) crystal structure of benzoate coenzyme A ligase | ||||||
Components | Benzoate-coenzyme A ligase | ||||||
Keywords | LIGASE | ||||||
Function / homology | Function and homology information acid-thiol ligase activity / CoA-ligase activity / secondary metabolite biosynthetic process / ATP binding Similarity search - Function | ||||||
Biological species | Rhodopseudomonas palustris (phototrophic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å | ||||||
Authors | Li, T.L. / Adhikari, K. | ||||||
Citation | Journal: Biomolecules / Year: 2020 Title: Chemoenzymatic Synthesis and Biological Evaluation for Bioactive Molecules Derived from Bacterial Benzoyl Coenzyme A Ligase and Plant Type III Polyketide Synthase. Authors: Adhikari, K. / Lo, I.W. / Chen, C.L. / Wang, Y.L. / Lin, K.H. / Zadeh, S.M. / Rattinam, R. / Li, Y.S. / Wu, C.J. / Li, T.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6m2o.cif.gz | 233.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6m2o.ent.gz | 182.8 KB | Display | PDB format |
PDBx/mmJSON format | 6m2o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6m2o_validation.pdf.gz | 443.2 KB | Display | wwPDB validaton report |
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Full document | 6m2o_full_validation.pdf.gz | 453.8 KB | Display | |
Data in XML | 6m2o_validation.xml.gz | 48.3 KB | Display | |
Data in CIF | 6m2o_validation.cif.gz | 74.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m2/6m2o ftp://data.pdbj.org/pub/pdb/validation_reports/m2/6m2o | HTTPS FTP |
-Related structure data
Related structure data | 6m2uC 4eatS S: Starting model for refinement C: citing same article (ref.) |
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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: 56683.098 Da / Num. of mol.: 2 / Mutation: T83A, H333A, I334A, G341D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic) Gene: badA / Production host: Rhodopseudomonas palustris (phototrophic) / References: UniProt: Q93TK0 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.08 % |
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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 pH 6.5 |
-Data collection
Diffraction | Mean temperature: 200 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å |
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: 1.57→29.516 Å / Num. obs: 140471 / % possible obs: 99.12 % / Redundancy: 3.8 % / CC1/2: 0.904 / Net I/σ(I): 32.95 |
Reflection shell | Resolution: 1.57→1.57 Å / CC1/2: 0.904 / CC star: 0.974 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4EAT Resolution: 1.57→29.516 Å / SU ML: 0.15 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 20.95
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.57→29.516 Å
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Refine LS restraints |
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LS refinement shell |
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