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Yorodumi- PDB-1xa4: Crystal structure of CaiB, a type III CoA transferase in carnitin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xa4 | ||||||
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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 | ||||||
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: 1.9 Å | ||||||
Authors | Stenmark, P. / Gurmu, D. / Nordlund, P. | ||||||
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 | 1xa4.cif.gz | 186.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xa4.ent.gz | 145 KB | Display | PDB format |
PDBx/mmJSON format | 1xa4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1xa4_validation.pdf.gz | 792.8 KB | Display | wwPDB validaton report |
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Full document | 1xa4_full_validation.pdf.gz | 798.1 KB | Display | |
Data in XML | 1xa4_validation.xml.gz | 35.7 KB | Display | |
Data in CIF | 1xa4_validation.cif.gz | 53.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xa/1xa4 ftp://data.pdbj.org/pub/pdb/validation_reports/xa/1xa4 | HTTPS FTP |
-Related structure data
Related structure data | 1xa3SC 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: 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 | ChemComp-SO4 / | #3: Chemical | #4: Chemical | ChemComp-COA / | #5: 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: 51.7 % |
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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: MAX II / Beamline: I711 / Wavelength: 1.09 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 13, 2004 |
Radiation | Monochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.09 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. all: 70549 / Num. obs: 70549 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.95 % / Biso Wilson estimate: 19.9 Å2 / Rsym value: 0.067 / Net I/σ(I): 7.71 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3.01 / Rsym value: 0.23 / % possible all: 95.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1XA3 Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.421 / SU ML: 0.072 / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.109 / 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: 19.01 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 1.9 Å / Num. reflection Rwork: 4715 / Total num. of bins used: 20 |