+Open data
-Basic information
Entry | Database: PDB / ID: 3wmd | ||||||
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Title | Crystal structure of epoxide hydrolase MonBI | ||||||
Components | Probable monensin biosynthesis isomerase | ||||||
Keywords | ISOMERASE / NTF2-like / Epoxide-opening cyclic ether formation | ||||||
Function / homology | SnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / isomerase activity / Roll / Alpha Beta / MonBI Function and homology information | ||||||
Biological species | Streptomyces cinnamonensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.999 Å | ||||||
Authors | Minami, A. / Ose, T. / Sato, K. / Oikawa, A. / Kuroki, K. / Maenaka, K. / Oguri, H. / Oikawa, H. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2014 Title: Allosteric regulation of epoxide opening cascades by a pair of epoxide hydrolases in monensin biosynthesis Authors: Minami, A. / Ose, T. / Sato, K. / Oikawa, A. / Kuroki, K. / Maenaka, K. / Oguri, H. / Oikawa, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wmd.cif.gz | 69.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wmd.ent.gz | 51.4 KB | Display | PDB format |
PDBx/mmJSON format | 3wmd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wm/3wmd ftp://data.pdbj.org/pub/pdb/validation_reports/wm/3wmd | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17808.322 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces cinnamonensis (bacteria) / Gene: monBI / Plasmid: pColdI / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: Q846W7 #2: 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: 1.65 Å3/Da / Density % sol: 25.39 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: 0.1M potassium phosphate, 20%(v/v) PEG6000, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1.000, 0.9300, 0.9797 | ||||||||||||
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jul 4, 2012 / Details: mirrors | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.999→50 Å / Num. obs: 16242 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 39 | ||||||||||||
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 5.2 / Num. unique all: 676 / % possible all: 83.9 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.999→31.398 Å / SU ML: 0.18 / σ(F): 1.35 / Phase error: 31.74 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.999→31.398 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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