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Yorodumi- PDB-4r9l: Structure of a thermostable elevenfold mutant of limonene epoxide... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4r9l | ||||||
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Title | Structure of a thermostable elevenfold mutant of limonene epoxide hydrolase from Rhodococcus erythropolis, containing two stabilizing disulfide bonds | ||||||
Components | Limonene-1,2-epoxide hydrolase | ||||||
Keywords | HYDROLASE / limonene epoxide hydrolase / NTF-2 fold / engineered / thermostable | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Floor, R.J. / Wijma, H.J. / Jekel, P.A. / Terwisscha van Scheltinga, A.C. / Dijkstra, B.W. / Janssen, D.B. | ||||||
Citation | Journal: Proteins / Year: 2015 Title: X-ray crystallographic validation of structure predictions used in computational design for protein stabilization. Authors: Floor, R.J. / Wijma, H.J. / Jekel, P.A. / Terwisscha van Scheltinga, A.C. / 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 | 4r9l.cif.gz | 109 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4r9l.ent.gz | 83.7 KB | Display | PDB format |
PDBx/mmJSON format | 4r9l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4r9l_validation.pdf.gz | 471.7 KB | Display | wwPDB validaton report |
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Full document | 4r9l_full_validation.pdf.gz | 474.9 KB | Display | |
Data in XML | 4r9l_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | 4r9l_validation.cif.gz | 29.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r9/4r9l ftp://data.pdbj.org/pub/pdb/validation_reports/r9/4r9l | HTTPS FTP |
-Related structure data
Related structure data | 4r9kC 1nwwS 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 19508.176 Da / Num. of mol.: 3 Mutation: I5C, S15P, A19K, T76K, E84C, T85V, G89C, S91C, N92K, Y96F, E124D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus erythropolis (bacteria) / Gene: limA / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: Q9ZAG3, limonene-1,2-epoxide hydrolase #2: Chemical | #3: 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: 2.07 Å3/Da / Density % sol: 40.44 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.4 Details: 1.44 M tri-sodium citrate, 50 mM sodium tartrate dihydrate, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 77 K | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.999 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 22, 2013 | |||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.999 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.8→44.25 Å / Num. obs: 45204 / % possible obs: 99.5 % / Observed criterion σ(F): 2.3 / Observed criterion σ(I): 2.3 / Redundancy: 3.5 % / Biso Wilson estimate: 19.9 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.042 / Net I/σ(I): 10 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1NWW Resolution: 1.8→44.25 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.805 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.11 / ESU R Free: 0.114 / 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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.115 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→44.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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