+Open data
-Basic information
Entry | Database: PDB / ID: 2wfl | ||||||
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Title | Crystal structure of polyneuridine aldehyde esterase | ||||||
Components | (POLYNEURIDINE-ALDEHYDE ESTERASE) x 2 | ||||||
Keywords | HYDROLASE / ALKALOID METABOLISM / MONOTERPENOID INDOLE ALKALOIDS / PNAE / 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 / Resolution: 2.1 Å | ||||||
Authors | Yang, L. / Hill, M. / Panjikar, S. / Wang, M. / 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 | 2wfl.cif.gz | 121.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wfl.ent.gz | 94.3 KB | Display | PDB format |
PDBx/mmJSON format | 2wfl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wfl_validation.pdf.gz | 427.4 KB | Display | wwPDB validaton report |
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Full document | 2wfl_full_validation.pdf.gz | 440.6 KB | Display | |
Data in XML | 2wfl_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 2wfl_validation.cif.gz | 23.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wf/2wfl ftp://data.pdbj.org/pub/pdb/validation_reports/wf/2wfl | HTTPS FTP |
-Related structure data
Related structure data | 2wfmC 3gzjC 1xklS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 2
NCS oper: (Code: given Matrix: (0.7085, 0.6818, 0.182), Vector: |
-Components
#1: Protein | Mass: 29767.490 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RAUVOLFIA SERPENTINA (serpentwood) / Plasmid: PQE-2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15PREP4 References: UniProt: Q9SE93, polyneuridine-aldehyde esterase | ||
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#2: Protein | Mass: 29843.611 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RAUVOLFIA SERPENTINA (serpentwood) / Plasmid: PQE-2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15PREP4 References: UniProt: Q9SE93, polyneuridine-aldehyde esterase | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53 % / Description: NONE |
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Crystal grow | pH: 6.8 Details: 0.20M BIS-TRIS, 0.25M LI2SO4, 25%POLYETHYLENE GLYCOL 3350, PH6.30., pH 6.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8 |
Detector | Type: MARRESEARCH / Detector: CCD / Details: DOUBLE CRYSTAL SI 111 |
Radiation | Monochromator: SILICON 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 36861 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 9.6 % / Biso Wilson estimate: 38.42 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 32.5 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 4.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1XKL Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / SU B: 6.78 / SU ML: 0.115 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.171 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.17 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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