[English] 日本語
Yorodumi- PDB-4hzg: Structure of haloalkane dehalogenase DhaA from Rhodococcus rhodochrous -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hzg | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of haloalkane dehalogenase DhaA from Rhodococcus rhodochrous | ||||||
Components | Haloalkane dehalogenase | ||||||
Keywords | HYDROLASE / Catalytic pentad / alpha/beta Hydrolase Fold / Halide binding / Hydrolytic dehalogenation | ||||||
Function / homology | Function and homology information haloalkane dehalogenase / haloalkane dehalogenase activity / response to toxic substance Similarity search - Function | ||||||
Biological species | Rhodococcus sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Stsiapanava, A. / Weiss, M.S. / Mesters, J.R. / Kuta Smatanova, I. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Crystallographic analysis of 1,2,3-trichloropropane biodegradation by the haloalkane dehalogenase DhaA31. Authors: Lahoda, M. / Mesters, J.R. / Stsiapanava, A. / Chaloupkova, R. / Kuty, M. / Damborsky, J. / Kuta Smatanova, I. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4hzg.cif.gz | 77.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4hzg.ent.gz | 56.9 KB | Display | PDB format |
PDBx/mmJSON format | 4hzg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hz/4hzg ftp://data.pdbj.org/pub/pdb/validation_reports/hz/4hzg | HTTPS FTP |
---|
-Related structure data
Related structure data | 3rk4C 4fwbC 3fbwS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 34110.867 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus sp. (bacteria) / Strain: NCIB 13064 / Gene: dhaA / Plasmid: pAQN / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P0A3G3, haloalkane dehalogenase |
---|---|
#2: Chemical | ChemComp-CL / |
#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: 41.31 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.75 Details: 39% PEG 4000, 100 mM sodium acetate, 8% 1,2,3-trichloropropane, pH 7.75, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 1.9 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Oct 14, 2011 |
Radiation | Monochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→22 Å / Num. all: 23843 / Num. obs: 20934 / % possible obs: 87.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 20.45 Å2 / Rmerge(I) obs: 0.158 / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 1.85→1.94 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 2 / Num. unique all: 3508 / % possible all: 81.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3FBW Resolution: 1.95→22 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.861 / SU B: 6.487 / SU ML: 0.179 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.285 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.533 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→22 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.95→2.001 Å / Total num. of bins used: 20
|