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Yorodumi- PDB-2b4k: Acetobacter turbidans alpha-amino acid ester hydrolase complexed ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2b4k | ||||||
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Title | Acetobacter turbidans alpha-amino acid ester hydrolase complexed with phenylglycine | ||||||
Components | Alpha-amino acid ester hydrolase | ||||||
Keywords | HYDROLASE / alpha-beta hydrolase | ||||||
Function / homology | Function and homology information alpha-amino-acid esterase / alpha-amino-acid esterase activity / dipeptidyl-peptidase activity Similarity search - Function | ||||||
Biological species | Acetobacter pasteurianus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||
Authors | Barends, T.R.M. / Polderman-Tijmes, J.J. / Jekel, P.A. / Williams, C. / Wybenga, G. / Janssen, D.B. / Dijkstra, B.W. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Acetobacter turbidans alpha-amino acid ester hydrolase: how a single mutation improves an antibiotic-producing enzyme. Authors: Barends, T.R. / Polderman-Tijmes, J.J. / Jekel, P.A. / Williams, C. / Wybenga, G. / Janssen, D.B. / Dijkstra, B.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2b4k.cif.gz | 422.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2b4k.ent.gz | 337.7 KB | Display | PDB format |
PDBx/mmJSON format | 2b4k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b4/2b4k ftp://data.pdbj.org/pub/pdb/validation_reports/b4/2b4k | HTTPS FTP |
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-Related structure data
Related structure data | 1nx9SC 1ryyC 2b9vC 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: 72947.469 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acetobacter pasteurianus (bacteria) / Gene: aehA / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: Q8VRK8 #2: Chemical | #3: Chemical | ChemComp-GOL / #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: 6.1 Å3/Da / Density % sol: 80 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: sodium citrate, PEG4000, phenylglycine, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 1, 2004 |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 3→40 Å / Num. all: 121384 / Num. obs: 121384 / % possible obs: 93.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.186 |
Reflection shell | Resolution: 3→3.11 Å / Rmerge(I) obs: 0.917 / % possible all: 91.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1NX9 Resolution: 3.3→15 Å / Cor.coef. Fo:Fc: 0.853 / Cor.coef. Fo:Fc free: 0.813 / SU B: 19.366 / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.669 / ESU R Free: 0.45 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.29 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.3→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.3→3.381 Å / Total num. of bins used: 20 /
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