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Yorodumi- PDB-6n5v: Crystal Structure of Strictosidine in complex with 1H-indole-4-et... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6n5v | ||||||
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Title | Crystal Structure of Strictosidine in complex with 1H-indole-4-ethanamine | ||||||
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 Similarity search - Function | ||||||
Biological species | Rauvolfia serpentina (serpentwood) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.549 Å | ||||||
Authors | Cai, Y. / Shao, N. / Xie, H. / Futamura, Y. / Panjikar, S. / Liu, H. / Zhu, H. / Osada, H. / Zou, H. | ||||||
Funding support | China, 1items
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Citation | Journal: to be published Title: Crystal Structure of Strictosidine in complex with 1H-indole-4-ethanamine Authors: Cai, Y. / Shao, N. / Xie, H. / Futamura, Y. / Panjikar, S. / Liu, H. / Zhu, H. / 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 | 6n5v.cif.gz | 132.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6n5v.ent.gz | 102.3 KB | Display | PDB format |
PDBx/mmJSON format | 6n5v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n5/6n5v ftp://data.pdbj.org/pub/pdb/validation_reports/n5/6n5v | HTTPS FTP |
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-Related structure data
Related structure data | 2fp8C 2fp9C 2fpbC 2fpcC 2v91S 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
#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) / Strain (production host): M15PREP4 / References: UniProt: P68175, strictosidine synthase #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: 3.58 Å3/Da / Density % sol: 68.8 % / Description: Hexagonal |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion / pH: 7.5 Details: 0.8 M potassium sodium tartrate tetrahydrate and 0.1 M HEPES, pH 7.4, 5 mg/mL strictosidine synthase, 3 mM 4-IEA (1H-indole-4-ethanamine) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 1, 2017 / Details: DCM |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.549→37.6 Å / Num. obs: 64264 / % possible obs: 95.2 % / Redundancy: 2.23 % / Biso Wilson estimate: 65 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.06 / Rrim(I) all: 0.064 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.55→2.7 Å / Redundancy: 2.27 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 10128 / CC1/2: 0.906 / Rrim(I) all: 0.839 / % possible all: 93.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2V91 Resolution: 2.549→37.6 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.15 / Phase error: 33.89
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 81 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.549→37.6 Å
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Refine LS restraints |
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LS refinement shell |
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