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Yorodumi- PDB-1xa3: Crystal structure of CaiB, a type III CoA transferase in carnitin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xa3 | ||||||
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Title | Crystal structure of CaiB, a type III CoA transferase in carnitine metabolism | ||||||
Components | Crotonobetainyl-CoA:carnitine CoA-transferase | ||||||
Keywords | TRANSFERASE / CaiB / carnitine / CoA transferase / CoA / Coenzyme A / interlocked / dimer / Bis-tris / Structural Proteomics in Europe / SPINE / Structural Genomics | ||||||
Function / homology | Function and homology information L-carnitine CoA-transferase / L-carnitine CoA-transferase activity / carnitine catabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å | ||||||
Authors | Stenmark, P. / Gurmu, D. / Nordlund, P. / Structural Proteomics in Europe (SPINE) | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Crystal Structure of CaiB, a Type-III CoA Transferase in Carnitine Metabolism Authors: Stenmark, P. / Gurmu, D. / Nordlund, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xa3.cif.gz | 181.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xa3.ent.gz | 149.8 KB | Display | PDB format |
PDBx/mmJSON format | 1xa3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xa/1xa3 ftp://data.pdbj.org/pub/pdb/validation_reports/xa/1xa3 | HTTPS FTP |
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-Related 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: 49700.777 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: caiB / Plasmid: PT73.3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3) References: UniProt: P31572, Transferases; Transferring sulfur-containing groups; CoA-transferases #2: Chemical | #3: Chemical | #4: 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: 2.6 Å3/Da / Density % sol: 53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: PEG 3350, Ammonium Sulphate, Glycerol, Sodium Chloride, Bis-tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.98 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 9, 2003 |
Radiation | Monochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→30 Å / Num. all: 76742 / Num. obs: 76742 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.76 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 5.82 |
Reflection shell | Resolution: 1.85→1.95 Å / Redundancy: 3.42 % / Mean I/σ(I) obs: 3.46 / Rsym value: 0.18 / % possible all: 89.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.85→30 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.181 / SU ML: 0.067 / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.105 / Stereochemistry target values: Engh & Huber
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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 WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.513 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→30 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 1.85 Å / Num. reflection Rwork: 4549 / Total num. of bins used: 20 |