[English] 日本語
Yorodumi- PDB-4ccw: Crystal structure of naproxen esterase (carboxylesterase NP) from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ccw | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of naproxen esterase (carboxylesterase NP) from Bacillus subtilis | ||||||
Components | CARBOXYL ESTERASE NP | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | BACILLUS SUBTILIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Rozeboom, H.J. / Godinho, L.F. / Nardini, M. / Quax, W.J. / Dijkstra, B.W. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2014 Title: Crystal Structures of Two Bacillus Carboxylesterases with Different Enantioselectivities. Authors: Rozeboom, H.J. / Godinho, L.F. / Nardini, M. / Quax, W.J. / Dijkstra, B.W. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4ccw.cif.gz | 132.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4ccw.ent.gz | 103.6 KB | Display | PDB format |
PDBx/mmJSON format | 4ccw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cc/4ccw ftp://data.pdbj.org/pub/pdb/validation_reports/cc/4ccw | HTTPS FTP |
---|
-Related structure data
Related structure data | 4ccyC 1c4xS 1iunS 1zoiS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 33871.289 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-300 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Strain: THAI I-8 / Production host: BACILLUS SUBTILIS (bacteria) / Strain (production host): I-85 / References: UniProt: Q59248, carboxylesterase |
---|---|
#2: Chemical | ChemComp-VKC / ( |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 40 % / Description: NONE |
---|---|
Crystal grow | Method: liquid diffusion / pH: 8 Details: LIQUID-LIQUID DIFFUSION WITH 80% PEG6000, 0.1 M TRIS PH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 3, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→40 Å / Num. obs: 28534 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 1.75→1.78 Å / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 5.4 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1ZOI, 1IUN, 1C4X Resolution: 1.75→39.97 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.913 / SU B: 5.935 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: BABINET MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.473 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→39.97 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|