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- PDB-7zk1: Crystal structure of cystinosin from Arabidopsis thaliana bound t... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7zk1 | ||||||
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Title | Crystal structure of cystinosin from Arabidopsis thaliana bound to sybody and nanobody | ||||||
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Function / homology | Lysosomal cystine transporter / Repeated motif present between transmembrane helices in cystinosin, yeast ERS1p, mannose-P-dolichol utilization defect 1, and other hypothetical proteins. / PQ-loop repeat / PQ loop repeat / plant-type vacuole / lysosomal membrane / Cystinosin homolog![]() | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Loebel, M. / Newstead, S. / Omari, K.E. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for proton coupled cystine transport by cystinosin. Authors: Lobel, M. / Salphati, S.P. / El Omari, K. / Wagner, A. / Tucker, S.J. / Parker, J.L. / Newstead, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 205 KB | Display | ![]() |
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PDB format | ![]() | 168.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7zkwC ![]() 7zkzC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 31902.965 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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#2: Antibody | Mass: 13888.493 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
#3: Antibody | Mass: 13651.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: ![]() ![]() ![]() |
#4: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.13 Å3/Da / Density % sol: 70.19 % |
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Crystal grow![]() | Temperature: 293 K / Method: lipidic cubic phase / pH: 5.5 Details: 27.5% PEG 500DME, 100 mM MES-NaOH, pH 5.50, 100 mM K-formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 20, 2021 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | |||||||||||||||||||||||||||
Reflection | Resolution: 2.65→79.99 Å / Num. obs: 28079 / % possible obs: 99.9 % / Redundancy: 20 % / CC1/2: 0.996 / Rmerge(I) obs: 0.542 / Rpim(I) all: 0.114 / Rrim(I) all: 0.554 / Net I/σ(I): 5.9 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 99.9
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Processing
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Refinement | Method to determine structure![]() ![]()
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Displacement parameters | Biso max: 131.86 Å2 / Biso mean: 84.8151 Å2 / Biso min: 33.68 Å2
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Refine analyze | Luzzati coordinate error obs: 0.49 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→79.99 Å
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LS refinement shell | Resolution: 2.65→2.68 Å
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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