+Open data
-Basic information
Entry | Database: PDB / ID: 3a2m | |||||||||
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Title | CRYSTAL STRUCTURE OF DBJA (WILD TYPE Type I) | |||||||||
Components | Haloalkane dehalogenase | |||||||||
Keywords | HYDROLASE / A/B-HYDROLASE | |||||||||
Function / homology | Function and homology information haloalkane dehalogenase / haloalkane dehalogenase activity / hydrolase activity / identical protein binding Similarity search - Function | |||||||||
Biological species | Bradyrhizobium japonicum (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å | |||||||||
Authors | Sato, Y. / Senda, T. | |||||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2010 Title: Enantioselectivity of haloalkane dehalogenases and its modulation by surface loop engineering Authors: Prokop, Z. / Sato, Y. / Brezovsky, J. / Mozga, T. / Chaloupkova, R. / Koudelakova, T. / Jerabek, P. / Stepankova, V. / Natsume, R. / van Leeuwen, J.G. / Janssen, D.B. / Florian, J. / Nagata, ...Authors: Prokop, Z. / Sato, Y. / Brezovsky, J. / Mozga, T. / Chaloupkova, R. / Koudelakova, T. / Jerabek, P. / Stepankova, V. / Natsume, R. / van Leeuwen, J.G. / Janssen, D.B. / Florian, J. / Nagata, Y. / Senda, T. / Damborsky, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3a2m.cif.gz | 140.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3a2m.ent.gz | 108 KB | Display | PDB format |
PDBx/mmJSON format | 3a2m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a2/3a2m ftp://data.pdbj.org/pub/pdb/validation_reports/a2/3a2m | HTTPS FTP |
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-Related structure data
Related structure data | 3a2lC 3a2nC 3afiC 3a1o 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: 34344.109 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bradyrhizobium japonicum (bacteria) / Strain: USDA110 / Gene: DBJA / Plasmid: PYBJA3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P59337, haloalkane dehalogenase #2: Polysaccharide | #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | VAL AND ASP WERE ADDED TO C-TERMINUS. THE DBJAWT CONSTRUCT CODES FOR RESIDUES 1-310 OF DBJA WITH C- ...VAL AND ASP WERE ADDED TO C-TERMINUS. THE DBJAWT CONSTRUCT CODES FOR RESIDUES 1-310 OF DBJA WITH C-TERMINUS FUSED TO A RESTRICTIO | |
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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: 2.36 Å3/Da / Density % sol: 47.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.9 Details: PEG 4000, PH 7.9, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 20, 2006 |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→33.7 Å / Num. obs: 55824 / % possible obs: 99.9 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 1.84→1.92 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.254 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3A1O 3a1o Resolution: 1.84→33.7 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.234 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 17.24 Å2
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Refinement step | Cycle: LAST / Resolution: 1.84→33.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.84→1.89 Å / Total num. of bins used: 20
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