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Yorodumi- PDB-1ehy: X-ray structure of the epoxide hydrolase from agrobacterium radio... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ehy | ||||||
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Title | X-ray structure of the epoxide hydrolase from agrobacterium radiobacter ad1 | ||||||
Components | PROTEIN (SOLUBLE EPOXIDE HYDROLASE) | ||||||
Keywords | HYDROLASE / ALPHA/BETA HYDROLASE FOLD / EPOXIDE DEGRADATION / EPICHLOROHYDRIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Agrobacterium tumefaciens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.1 Å | ||||||
Authors | Nardini, M. / Ridder, I.S. / Rozeboom, H.J. / Kalk, K.H. / Rink, R. / Janssen, D.B. / Dijkstra, B.W. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1999 Title: The x-ray structure of epoxide hydrolase from Agrobacterium radiobacter AD1. An enzyme to detoxify harmful epoxides. Authors: Nardini, M. / Ridder, I.S. / Rozeboom, H.J. / Kalk, K.H. / Rink, R. / Janssen, D.B. / Dijkstra, B.W. #1: Journal: Tetrahedron / Year: 1998 Title: Enantioselectivity of a Recombinant Epoxide Hydrolase from Agrobacterium Radiobacter Authors: Lutje Spelberg, J.H. / Rink, R. / Kellogg, R.M. / Janssen, D.B. #2: Journal: J.Biol.Chem. / Year: 1997 Title: Primary Structure and Catalytic Mechanism of the Epoxide Hydrolase from Agrobacterium Radiobacter AD1 Authors: Rink, R. / Fennema, M. / Smids, M. / Dehmel, U. / Janssen, D.B. #3: Journal: Biochemistry / Year: 1998 Title: Kinetic Mechanism of the Enantioselective Conversion of Styrene Oxide by Epoxide Hydrolase from Agrobacterium Radiodacter AD1 Authors: Jacobs, M.H.J. / Van Den Wijngaard, A.J. / Pentenga, M. / Janssen, D.B. #4: Journal: To be Published Title: Mutation of Tyrosine Residues Involved in the Alkylation Half Reaction of Epoxide Hydrolase from Agrobacterium Radiodacter AD1 Results in Improved Enantioselectivity Authors: Rink, R. / Lutje Spelberg, J.H. / Pieters, R.J. / Kingma, J. / Nardini, M. / Kellogg, R.M. / Dijkstra, B.W. / Janssen, D.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ehy.cif.gz | 247.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ehy.ent.gz | 201.2 KB | Display | PDB format |
PDBx/mmJSON format | 1ehy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ehy_validation.pdf.gz | 450.3 KB | Display | wwPDB validaton report |
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Full document | 1ehy_full_validation.pdf.gz | 465.3 KB | Display | |
Data in XML | 1ehy_validation.xml.gz | 46.8 KB | Display | |
Data in CIF | 1ehy_validation.cif.gz | 66.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eh/1ehy ftp://data.pdbj.org/pub/pdb/validation_reports/eh/1ehy | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 34074.656 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: AD1 / Plasmid: PGELAF+ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O31243, soluble epoxide hydrolase #2: Chemical | ChemComp-K / #3: Water | ChemComp-HOH / | Compound details | DUE TO A CRYSTAL CONTACT BETWEEN LOOP RESIDUES 246-251 OF MONOMERS C AND D AND MONOMERS A AND B, IN ...DUE TO A CRYSTAL CONTACT BETWEEN LOOP RESIDUES 246-251 OF MONOMERS C AND D AND MONOMERS A AND B, IN ALL 4 MONOMERS THE CATALYTIC ASP 246 IS PULLED OUT FROM THE ACTIVE SITE, SO ALLOWING RESIDUE GLN 134 TO MOVE INTO THE ACTIVE SITE. | |
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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: 2.57 Å3/Da / Density % sol: 52 % | |||||||||||||||
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Crystal grow | pH: 7 / Details: 1.8 M KH2PO4/K2HPO4, pH 7.0 | |||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→25 Å / Num. obs: 73445 / % possible obs: 91.5 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 2.1→2.14 Å / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.57 / % possible all: 82 |
Reflection | *PLUS Num. measured all: 222880 |
Reflection shell | *PLUS % possible obs: 82 % |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 2.1→25 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0 Details: BULK SOLVENT CORRECTION USED DURING THE REFINEMENT IN ALL 4 MOLECULES IN THE ASYMMETRIC UNIT THE LOOP 246-251 SHOWS POOR ELECTRON DENSITY. HOWEVER CLEAR ELECTRON DENSITY IS PRESENT FOR THE ...Details: BULK SOLVENT CORRECTION USED DURING THE REFINEMENT IN ALL 4 MOLECULES IN THE ASYMMETRIC UNIT THE LOOP 246-251 SHOWS POOR ELECTRON DENSITY. HOWEVER CLEAR ELECTRON DENSITY IS PRESENT FOR THE SS BOND BETWEEN RESIDUES C248 AND D248. DUE TO A SLIGHTLY DIFFERENT CONFORMATION OF THAT LOOP IN MONOMER A, NO SS BOND IS OBSERVED BETWEEN RESIDUES A248 AND B248
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Displacement parameters | Biso mean: 28.3 Å2 | ||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→25 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.16 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 12
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 25 Å / σ(F): 0 / % reflection Rfree: 5.2 % / Rfactor obs: 0.19 / Rfactor Rwork: 0.19 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 28.3 Å2 | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.1 Å / Rfactor Rfree: 0.318 / % reflection Rfree: 4.5 % / Rfactor Rwork: 0.286 |