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Yorodumi- PDB-7t5j: Crystal Structure of Strictosidine Synthase in complex with S-IPA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7t5j | ||||||
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Title | Crystal Structure of Strictosidine Synthase in complex with S-IPA (2-(1H-indol-3-yl) propan-1-amine) | ||||||
Components | Strictosidine synthase | ||||||
Keywords | LYASE / ALKALOID METABOLISM / SIX BLADED BETA PROPELLER FOLD / STR1 / VACUOLE / SYNTHASE / GLYCOPROTEIN | ||||||
Function / homology | Function and homology information strictosidine synthase / strictosidine synthase activity / alkaloid metabolic process / vacuole / biosynthetic process / endomembrane system / hydrolase activity Similarity search - Function | ||||||
Biological species | Rauvolfia serpentina (serpentwood) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.86 Å | ||||||
Authors | Liu, H. / Panjikar, S. / Futamura, Y. / Shao, N. / Osada, H. / Zou, H. | ||||||
Funding support | China, 1items
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Citation | Journal: to be published Title: beta-Branched Tryptamine Provoked Non Sandwich-Like-Mode Catalysis of Strictosidine Synthase to Antimalarial Indole Alkaloids Authors: Liu, H. / Panjikar, S. / Futamura, Y. / Shao, N. / Osada, H. / Zou, H. #1: Journal: Plant Cell / Year: 2006 Title: The structure of Rauvolfia serpentina strictosidine synthase is a novel six-bladed beta-propeller fold in plant proteins. Authors: Ma, X. / Panjikar, S. / Koepke, J. / Loris, E. / Stoeckigt, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7t5j.cif.gz | 254.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7t5j.ent.gz | 206.6 KB | Display | PDB format |
PDBx/mmJSON format | 7t5j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7t5j_validation.pdf.gz | 814.5 KB | Display | wwPDB validaton report |
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Full document | 7t5j_full_validation.pdf.gz | 825.7 KB | Display | |
Data in XML | 7t5j_validation.xml.gz | 23.5 KB | Display | |
Data in CIF | 7t5j_validation.cif.gz | 31.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t5/7t5j ftp://data.pdbj.org/pub/pdb/validation_reports/t5/7t5j | HTTPS FTP |
-Related structure data
Related structure data | 2fp8S 7l1l 7l1n 7l1o S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 35207.309 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rauvolfia serpentina (serpentwood) / Gene: STR1 / Plasmid: PQE-2 / Production host: Escherichia coli (E. coli) / References: UniProt: P68175, strictosidine synthase #2: Chemical | ChemComp-XLJ / ( | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 3.78 Å3/Da / Density % sol: 67.47 % / Description: Hexagonal |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.8 M POTASSIUM SODIUM TARTRATE TETRAHYDRATE AND 0.1 M HEPES, PH 7.4, 5 MG/ML STRICTOSIDINE and 3 mM S-IPA (2-(1H-indol-3-yl) propan-1-amine) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 12, 2018 / Details: DCM |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.86→20 Å / Num. obs: 22563 / % possible obs: 93.8 % / Redundancy: 5 % / Biso Wilson estimate: 80.97 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.06 / Rrim(I) all: 0.136 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.86→3.02 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.628 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 3456 / CC1/2: 0.93 / Rpim(I) all: 0.439 / Rrim(I) all: 0.698 / % possible all: 98.6 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2FP8 Resolution: 2.86→20 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.944 / SU B: 34.356 / SU ML: 0.295 / Cross valid method: THROUGHOUT / ESU R: 0.802 / ESU R Free: 0.314 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 85.89 Å2
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Refinement step | Cycle: 1 / Resolution: 2.86→20 Å
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