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Yorodumi- PDB-6pcd: Crystal structure of beta-ketoadipyl-CoA thiolase mutant (C90S-H3... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6pcd | ||||||
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Title | Crystal structure of beta-ketoadipyl-CoA thiolase mutant (C90S-H356A) in complex Octanoyl coenzyme A | ||||||
Components | Beta-ketoadipyl-CoA thiolase | ||||||
Keywords | TRANSFERASE / aromatic pollutant catabolism / degradative enzymes | ||||||
Function / homology | Function and homology information 3-oxoadipyl-CoA thiolase / 3-oxoadipyl-CoA thiolase activity / acetyl-CoA C-acyltransferase activity / 3,4-dihydroxybenzoate catabolic process / phenylacetate catabolic process / fatty acid beta-oxidation Similarity search - Function | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å | ||||||
Authors | Sukritee, B. / Panjikar, S. | ||||||
Citation | Journal: J Struct Biol X / Year: 2020 Title: Structural basis for differentiation between two classes of thiolase: Degradative vs biosynthetic thiolase. Authors: Bhaskar, S. / Steer, D.L. / Anand, R. / Panjikar, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6pcd.cif.gz | 626.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pcd.ent.gz | 499.6 KB | Display | PDB format |
PDBx/mmJSON format | 6pcd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6pcd_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 6pcd_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 6pcd_validation.xml.gz | 72.8 KB | Display | |
Data in CIF | 6pcd_validation.cif.gz | 109.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pc/6pcd ftp://data.pdbj.org/pub/pdb/validation_reports/pc/6pcd | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 44420.578 Da / Num. of mol.: 4 / Mutation: C90S, H356A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440) (bacteria) Strain: ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440 / Gene: pcaF-I, PP_1377 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: Q88N39, acetyl-CoA C-acyltransferase, 3-oxoadipyl-CoA thiolase |
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-Non-polymers , 6 types, 1757 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-CL / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.16 Å3/Da / Density % sol: 43.18 % / Description: Plate type |
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Crystal grow | Temperature: 299 K / Method: vapor diffusion / Details: lithium chloride,PEG 6000,tris (pH- 7.3-8.3) / PH range: 7.3-8.3 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 25, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 1.37→80 Å / Num. obs: 677103 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 12.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.063 / Rrim(I) all: 0.074 / Net I/σ(I): 11.96 |
Reflection shell | Resolution: 1.37→1.45 Å / Redundancy: 3.29 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.09 / Num. unique obs: 108090 / CC1/2: 0.71 / Rrim(I) all: 0.656 / % possible all: 98.1 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: native structure Resolution: 1.37→19.991 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.97 / WRfactor Rfree: 0.172 / WRfactor Rwork: 0.138 / SU B: 2.471 / SU ML: 0.042 / Average fsc free: 0.9275 / Average fsc work: 0.9563 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.047 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.824 Å2
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Refinement step | Cycle: LAST / Resolution: 1.37→19.991 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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