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Yorodumi- PDB-6i1r: Crystal structure of CMP bound CST in an outward facing conformation -
+Open data
-Basic information
Entry | Database: PDB / ID: 6i1r | ||||||
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Title | Crystal structure of CMP bound CST in an outward facing conformation | ||||||
Components | CMP-sialic acid transporter 1 | ||||||
Keywords | MEMBRANE PROTEIN / CMP-sialic acid transporter / Secondary active transporter / Nucleotide sugar transporter / SLC35A1 | ||||||
Function / homology | pyrimidine nucleotide-sugar transmembrane transporter activity / sialic acid transmembrane transporter activity / Nucleotide-sugar transporter / Nucleotide-sugar transporter / Golgi membrane / identical protein binding / CYTIDINE-5'-MONOPHOSPHATE / CMP-sialic acid transporter 1 Function and homology information | ||||||
Biological species | Zea mays (maize) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Nji, E. / Gulati, A. / Qureshi, A.A. / Drew, D. | ||||||
Funding support | Sweden, 1items
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Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2019 Title: Structural basis for the delivery of activated sialic acid into Golgi for sialyation. Authors: Nji, E. / Gulati, A. / Qureshi, A.A. / Coincon, M. / Drew, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6i1r.cif.gz | 133.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6i1r.ent.gz | 102.7 KB | Display | PDB format |
PDBx/mmJSON format | 6i1r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i1/6i1r ftp://data.pdbj.org/pub/pdb/validation_reports/i1/6i1r | HTTPS FTP |
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-Related structure data
Related structure data | 6i1zC 5i20S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 1 / Auth seq-ID: 1 - 313 / Label seq-ID: 1 - 313
NCS oper:
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-Components
#1: Protein | Mass: 36518.980 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zea mays (maize) / Gene: 100274139, ZEAMMB73_Zm00001d046060 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: B4FZ94 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.16 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 5 Details: 400 mM Ammonium sulfate, 100 mM Lithium sulfate, 100 mM NaCl, 100 mM Sodium citrate, 30% PEG 300, tert butanol and 1.2 mM CMP |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 15, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.8→50 Å / Num. obs: 20716 / % possible obs: 100 % / Redundancy: 7 % / Rpim(I) all: 0.076 / Rrim(I) all: 0.201 / Rsym value: 0.185 / Net I/σ(I): 7.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5i20 Resolution: 2.8→45.83 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.925 / SU B: 10.686 / SU ML: 0.225 / SU R Cruickshank DPI: 5.5881 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 5.588 / ESU R Free: 0.36 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 140.76 Å2 / Biso mean: 71.742 Å2 / Biso min: 31.12 Å2
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Refinement step | Cycle: final / Resolution: 2.8→45.83 Å
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Refine LS restraints |
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Refine LS restraints NCS | Number: 2384 / Type: TIGHT THERMAL / Rms dev position: 5.53 Å / Weight position: 0.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.873 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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