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Yorodumi- PDB-7zk1: Crystal structure of cystinosin from Arabidopsis thaliana bound t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zk1 | ||||||
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Title | Crystal structure of cystinosin from Arabidopsis thaliana bound to sybody and nanobody | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / Cystinosin / PQ-loop protein / proton coupling / cystine transport | ||||||
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 Function and homology information | ||||||
Biological species | Arabidopsis thaliana (thale cress) Lama glama (llama) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.65 Å | ||||||
Authors | Loebel, M. / Newstead, S. / Omari, K.E. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nat Commun / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zk1.cif.gz | 205 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zk1.ent.gz | 168.4 KB | Display | PDB format |
PDBx/mmJSON format | 7zk1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zk1_validation.pdf.gz | 411.8 KB | Display | wwPDB validaton report |
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Full document | 7zk1_full_validation.pdf.gz | 421.4 KB | Display | |
Data in XML | 7zk1_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | 7zk1_validation.cif.gz | 17.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zk/7zk1 ftp://data.pdbj.org/pub/pdb/validation_reports/zk/7zk1 | HTTPS FTP |
-Related structure data
Related structure data | 7zkwC 7zkzC C: citing same article (ref.) |
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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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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.) Arabidopsis thaliana (thale cress) / Gene: At5g40670, MNF13.23 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): BJ5460 / References: UniProt: P57758 |
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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.) Lama glama (llama) / Production host: Escherichia coli MC1061 (bacteria) |
#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: Escherichia coli (E. coli) |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9999 Å | |||||||||||||||||||||||||||
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: 0.9999 Å / Relative weight: 1 | |||||||||||||||||||||||||||
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
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.65→79.99 Å / SU R Cruickshank DPI: 0.391 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.391 / SU Rfree Blow DPI: 0.286 / SU Rfree Cruickshank DPI: 0.289
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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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