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Yorodumi- PDB-2jbw: Crystal Structure of the 2,6-dihydroxy-pseudo-oxynicotine Hydrolase. -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jbw | ||||||
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Title | Crystal Structure of the 2,6-dihydroxy-pseudo-oxynicotine Hydrolase. | ||||||
Components | 2,6-DIHYDROXY-PSEUDO-OXYNICOTINE HYDROLASE | ||||||
Keywords | HYDROLASE / ALPHA/BETA HYDROLASE / META-CLEAVAGE PATHWAY / RETRO- FRIEDEL- CRAFTS ACYLATION / NICOTINE DEGRADATION / HYPOTHETICAL PROTEIN / PLASMID / CATALYTIC TRIAD / C-C BOND CLEAVAGE | ||||||
Function / homology | Function and homology information 2,6-dihydroxypseudooxynicotine hydrolase / nicotine catabolic process / alkaloid metabolic process / hydrolase activity Similarity search - Function | ||||||
Biological species | ARTHROBACTER NICOTINOVORANS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å | ||||||
Authors | Schleberger, C. / Sachelaru, P. / Brandsch, R. / Schulz, G.E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Structure and Action of a Cc Bond Cleaving Alpha/Beta-Hydrolase Involved in Nicotine Degration. Authors: Schleberger, C. / Sachelaru, P. / Brandsch, R. / Schulz, G.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jbw.cif.gz | 449.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jbw.ent.gz | 387.6 KB | Display | PDB format |
PDBx/mmJSON format | 2jbw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jb/2jbw ftp://data.pdbj.org/pub/pdb/validation_reports/jb/2jbw | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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-Components
#1: Protein | Mass: 43861.480 Da / Num. of mol.: 4 / Fragment: RESIDUES 1-365 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ARTHROBACTER NICOTINOVORANS (bacteria) / Plasmid: PH6EX3.DHPONH / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: Q93NG6, EC: 3.7.1.- #2: Chemical | ChemComp-NA / #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: 2.3 Å3/Da / Density % sol: 46 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 8.8 Details: PROTEINSOLUTION: 50 MM TRIS-HCL PH 7.4, 200 MM NACL, 0.5 M TCEP RESERVOIR: 35% PEG 10000, O.1 M TRIS-HCL PH 8.8 HANGING DROP, MIXED 1:1, MICROSEEDING |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→35 Å / Num. obs: 172409 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Biso Wilson estimate: 33.2 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2.09→2.16 Å / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3.3 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.26 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.219 / ESU R Free: 0.19 / 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: 37.89 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→30 Å
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Refine LS restraints |
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