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- PDB-6n5v: Crystal Structure of Strictosidine in complex with 1H-indole-4-et... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6n5v | ||||||
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Title | Crystal Structure of Strictosidine in complex with 1H-indole-4-ethanamine | ||||||
![]() | Strictosidine synthase | ||||||
![]() | LYASE / ALKALOID METABOLISM / SIX BLADED BETA PROPELLER FOLD / STR1 / VACUOLE / SYNTHASE / GLYCOPROTEIN | ||||||
Function / homology | ![]() strictosidine synthase / strictosidine synthase activity / alkaloid metabolic process / vacuole / biosynthetic process / endomembrane system / hydrolase activity Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cai, Y. / Shao, N. / Xie, H. / Futamura, Y. / Panjikar, S. / Liu, H. / Zhu, H. / Osada, H. / Zou, H. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 132.8 KB | Display | ![]() |
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PDB format | ![]() | 102.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 850.3 KB | Display | ![]() |
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Full document | ![]() | 859.4 KB | Display | |
Data in XML | ![]() | 23.5 KB | Display | |
Data in CIF | ![]() | 32 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2fp8C ![]() 2fp9C ![]() 2fpbC ![]() 2fpcC ![]() 2v91S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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