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Yorodumi- PDB-1xvu: Crystal Structure of CaiB mutant D169A in complex with Coenzyme A -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xvu | ||||||
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Title | Crystal Structure of CaiB mutant D169A in complex with Coenzyme A | ||||||
Components | Crotonobetainyl-CoA:carnitine CoA-transferase | ||||||
Keywords | TRANSFERASE / CaiB / CoA transferase / Crotonobetainly CoA / Asp mutant | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Rangarajan, E.S. / Li, Y. / Iannuzzi, P. / Cygler, M. / Matte, A. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Crystal Structure of Escherichia coli Crotonobetainyl-CoA: Carnitine CoA-Transferase (CaiB) and Its Complexes with CoA and Carnitinyl-CoA. Authors: Rangarajan, E.S. / Li, Y. / Iannuzzi, P. / Cygler, M. / Matte, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xvu.cif.gz | 92.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xvu.ent.gz | 69.2 KB | Display | PDB format |
PDBx/mmJSON format | 1xvu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xv/1xvu ftp://data.pdbj.org/pub/pdb/validation_reports/xv/1xvu | HTTPS FTP |
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-Related structure data
Related structure data | 1xk6SC 1xk7C 1xvtC 1xvvC 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: 45408.828 Da / Num. of mol.: 1 / Mutation: D169A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: caiB / Plasmid: pGEX-4T1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: P31572, Transferases; Transferring sulfur-containing groups; CoA-transferases |
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#2: Chemical | ChemComp-COA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.6 Å3/Da / Density % sol: 65.52 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion / pH: 7 Details: 1.35M Sodium citrate, 0.1M Tris-Cl (pH 7.0), VAPOR DIFFUSION, temperature 21K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 23, 2004 |
Radiation | Monochromator: Silicone / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 25311 / Num. obs: 24976 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rsym value: 0.061 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 5.9 / Rsym value: 0.412 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1XK6 Resolution: 2.4→43.44 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.923 / SU B: 17.566 / SU ML: 0.192 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.262 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.816 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→43.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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