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- PDB-6gne: Catalytic domain of Starch Synthase IV from Arabidopsis thaliana ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6gne | |||||||||
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Title | Catalytic domain of Starch Synthase IV from Arabidopsis thaliana bound to ADP and acarbose | |||||||||
![]() | Probable starch synthase 4, chloroplastic/amyloplastic | |||||||||
![]() | TRANSFERASE / Glycosyl Transferase / Starch Synthase / Acarbose / ADP | |||||||||
Function / homology | ![]() starch synthase (glycosyl-transferring) / alpha-1,4-glucan synthase activity / starch synthase activity / starch biosynthetic process / amyloplast / starch metabolic process / glycogen (starch) synthase activity / chloroplast Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Cuesta-Seijo, J.A. / Ruzanski, C. / Krucewicz, K. / Striebeck, A. / Palcic, M.M. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal Structures of theCatalyticDomain ofArabidopsis thalianaStarch Synthase IV, of Granule Bound Starch Synthase From CLg1 and of Granule Bound Starch Synthase I ofCyanophora ...Title: Crystal Structures of theCatalyticDomain ofArabidopsis thalianaStarch Synthase IV, of Granule Bound Starch Synthase From CLg1 and of Granule Bound Starch Synthase I ofCyanophora paradoxaIllustrate Substrate Recognition in Starch Synthases. Authors: Nielsen, M.M. / Ruzanski, C. / Krucewicz, K. / Striebeck, A. / Cenci, U. / Ball, S.G. / Palcic, M.M. / Cuesta-Seijo, J.A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 409.1 KB | Display | ![]() |
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PDB format | ![]() | 333.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 36.5 KB | Display | |
Data in CIF | ![]() | 50.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6gnfC ![]() 6gngC ![]() 2qzsS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 23 - 514 / Label seq-ID: 8 - 499
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Components
#1: Protein | Mass: 57296.816 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q0WVX5, starch synthase (glycosyl-transferring) #2: Polysaccharide | #3: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.71 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop Details: 0.2 M Li2SO4, 0.1 M Bis-tris pH 5.5, 25% PEG3350, ZnCl2, ADP, acarbose |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 6, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→200 Å / Num. obs: 32689 / % possible obs: 93.6 % / Redundancy: 6.1 % / CC1/2: 0.996 / Rrim(I) all: 0.134 / Net I/σ(I): 11.93 |
Reflection shell | Resolution: 2.55→2.7 Å / Redundancy: 2.8 % / Num. unique obs: 4558 / CC1/2: 0.608 / Rrim(I) all: 0.871 / % possible all: 84.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2QZS Resolution: 2.55→41.87 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.927 / SU B: 20.373 / SU ML: 0.217 / Cross valid method: THROUGHOUT / ESU R Free: 0.302 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.961 Å2
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Refinement step | Cycle: 1 / Resolution: 2.55→41.87 Å
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Refine LS restraints |
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