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Yorodumi- PDB-3gzj: Crystal Structure of Polyneuridine Aldehyde Esterase Complexed wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gzj | ||||||
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Title | Crystal Structure of Polyneuridine Aldehyde Esterase Complexed with 16-epi-Vellosimine | ||||||
Components | Polyneuridine-aldehyde esterase | ||||||
Keywords | HYDROLASE / hydrolase superfamily / Alkaloid metabolism / Serine esterase | ||||||
Function / homology | Function and homology information polyneuridine-aldehyde esterase / polyneuridine-aldehyde esterase activity / indole alkaloid metabolic process / jasmonic acid metabolic process / methyl salicylate esterase activity / methyl jasmonate esterase activity / salicylic acid metabolic process / methyl indole-3-acetate esterase activity Similarity search - Function | ||||||
Biological species | Rauvolfia serpentina (serpentwood) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.19 Å | ||||||
Authors | Yang, L. / Hill, M. / Wang, M. / Panjikar, S. / Stoeckigt, J. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2009 Title: Structural basis and enzymatic mechanism of the biosynthesis of C9- from C10-monoterpenoid indole alkaloids Authors: Yang, L. / Hill, M. / Wang, M. / Panjikar, S. / Stockigt, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gzj.cif.gz | 258 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gzj.ent.gz | 209.5 KB | Display | PDB format |
PDBx/mmJSON format | 3gzj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3gzj_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 3gzj_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 3gzj_validation.xml.gz | 51.4 KB | Display | |
Data in CIF | 3gzj_validation.cif.gz | 69.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gz/3gzj ftp://data.pdbj.org/pub/pdb/validation_reports/gz/3gzj | HTTPS FTP |
-Related structure data
Related structure data | 2wflSC 2wfmC 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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2 |
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4 |
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5 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 1
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-Components
#1: Protein | Mass: 29011.629 Da / Num. of mol.: 5 / Mutation: A244H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rauvolfia serpentina (serpentwood) / Plasmid: pREP4 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 References: UniProt: Q9SE93, polyneuridine-aldehyde esterase #2: Chemical | ChemComp-EVS / #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: 46.52 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: PEG 3350, 0.20M Bis-Tris, 0.25M Lis2SO4, pH 6.3, vapor diffusion, hanging drop, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 18, 2007 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→20 Å / Num. all: 66881 / Num. obs: 66881 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 44.6 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2.19→2.32 Å / Redundancy: 3 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 2.2 / Num. unique all: 10364 / Rsym value: 0.425 / % possible all: 93.9 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2WFL Resolution: 2.19→20 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.898 / Occupancy max: 1 / Occupancy min: 1 / SU B: 16.041 / SU ML: 0.201 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.321 / ESU R Free: 0.253 / 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 max: 342.13 Å2 / Biso mean: 27.852 Å2 / Biso min: 7.26 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.19→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: E / Ens-ID: 1 / Number: 524 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.192→2.249 Å / Total num. of bins used: 20
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