+Open data
-Basic information
Entry | Database: PDB / ID: 1nu3 | ||||||
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Title | Limonene-1,2-epoxide hydrolase in complex with valpromide | ||||||
Components | limonene-1,2-epoxide hydrolase | ||||||
Keywords | HYDROLASE / PROTEIN-LIGAND COMPLEX | ||||||
Function / homology | Function and homology information limonene-1,2-epoxide hydrolase / limonene-1,2-epoxide hydrolase activity Similarity search - Function | ||||||
Biological species | Rhodococcus erythropolis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.75 Å | ||||||
Authors | Arand, M. / Hallberg, B.M. / Zou, J. / Bergfors, T. / Oesch, F. / van der Werf, M.J. / de Bont, J.A.M. / Jones, T.A. / Mowbray, S.L. | ||||||
Citation | Journal: EMBO J. / Year: 2003 Title: Structure of Rhodococcus erythropolis limonene-1,2-epoxide hydrolase reveals a novel active site Authors: Arand, M. / Hallberg, B.M. / Zou, J. / Bergfors, T. / Oesch, F. / van der Werf, M.J. / de Bont, J.A.M. / Jones, T.A. / Mowbray, S.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nu3.cif.gz | 73.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nu3.ent.gz | 58.6 KB | Display | PDB format |
PDBx/mmJSON format | 1nu3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nu3_validation.pdf.gz | 457.9 KB | Display | wwPDB validaton report |
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Full document | 1nu3_full_validation.pdf.gz | 459.5 KB | Display | |
Data in XML | 1nu3_validation.xml.gz | 17.1 KB | Display | |
Data in CIF | 1nu3_validation.cif.gz | 24.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nu/1nu3 ftp://data.pdbj.org/pub/pdb/validation_reports/nu/1nu3 | HTTPS FTP |
-Related 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: 16692.131 Da / Num. of mol.: 2 / Mutation: T2A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus erythropolis (bacteria) / Gene: limA / Plasmid: pGEF-LEH / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q9ZAG3, limonene-1,2-epoxide hydrolase #2: Chemical | ChemComp-MES / | #3: Chemical | #4: 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: 1.9 Å3/Da / Density % sol: 34.67 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 Details: PEG 6000, LiCl, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, sitting 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: MAX II / Beamline: I711 / Wavelength: 0.944 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 18, 2002 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.944 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→29 Å / Num. all: 29009 / Num. obs: 29009 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Redundancy: 3.9 % / Rsym value: 0.056 / Net I/σ(I): 20.7 |
Reflection shell | Resolution: 1.75→1.8 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 12.2 / Rsym value: 0.107 / % possible all: 97.5 |
Reflection | *PLUS Lowest resolution: 30 Å / Rmerge(I) obs: 0.056 |
Reflection shell | *PLUS % possible obs: 97.5 % / Rmerge(I) obs: 0.107 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.75→29 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / SU B: 1.961 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.108 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.292 Å2
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Refine analyze | Luzzati coordinate error obs: 0.051 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.796 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Lowest resolution: 29 Å / Rfactor Rfree: 0.195 / Rfactor Rwork: 0.158 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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