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Yorodumi- PDB-7zkz: Crystal structure of cystinosin from Arabidopsis thaliana bound t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zkz | ||||||
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Title | Crystal structure of cystinosin from Arabidopsis thaliana bound to two nanobodies | ||||||
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) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.329 Å | ||||||
Authors | Loebel, M. / Newstead, S. | ||||||
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 | 7zkz.cif.gz | 205.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zkz.ent.gz | 163.9 KB | Display | PDB format |
PDBx/mmJSON format | 7zkz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zk/7zkz ftp://data.pdbj.org/pub/pdb/validation_reports/zk/7zkz | HTTPS FTP |
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-Related structure data
Related structure data | 7zk1SC 7zkwC S: Starting model for refinement 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) / Variant (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: 13157.398 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) |
#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: 3.24 Å3/Da / Density % sol: 62.04 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 5.75 Details: 28% PEG 500DME, 100 mM MES-NaOH, pH 5.75, 150 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: I04 / Wavelength: 0.9795 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 25, 2021 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.329→104.76 Å / Num. obs: 31727 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 61.36 Å2 / Rpim(I) all: 0.072 / Rrim(I) all: 0.185 / Net I/σ(I): 7.9 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7ZK1 Resolution: 2.329→20.79 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.924 / SU R Cruickshank DPI: 0.269 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.26 / SU Rfree Blow DPI: 0.211 / SU Rfree Cruickshank DPI: 0.216
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Displacement parameters | Biso max: 131.19 Å2 / Biso mean: 66.88 Å2 / Biso min: 43.51 Å2
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Refine analyze | Luzzati coordinate error obs: 0.38 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.329→20.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.33→2.35 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
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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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