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Yorodumi- PDB-5jql: Crystal Structure of Phosphatidic acid Transporter Ups1/Mdm35 Voi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jql | ||||||
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Title | Crystal Structure of Phosphatidic acid Transporter Ups1/Mdm35 Void of Bound Phospholipid from Saccharomyces Cerevisiae at 2.9 Angstroms Resolution | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / Lipid Transport | ||||||
Function / homology | Function and homology information TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / phosphatidic acid transfer activity / cardiolipin metabolic process / positive regulation of phosphatidylcholine biosynthetic process / mitochondrial respiratory chain complex assembly / intermembrane lipid transfer / phospholipid transport / phospholipid translocation / mitochondrion organization / mitochondrial intermembrane space ...TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / phosphatidic acid transfer activity / cardiolipin metabolic process / positive regulation of phosphatidylcholine biosynthetic process / mitochondrial respiratory chain complex assembly / intermembrane lipid transfer / phospholipid transport / phospholipid translocation / mitochondrion organization / mitochondrial intermembrane space / mitochondrial inner membrane / lipid binding / mitochondrion / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å | ||||||
Authors | Lu, J. / Chan, K.C. / Zhai, Y. / Fan, J. / Sun, F. | ||||||
Funding support | China, 1items
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Citation | Journal: Commun Biol / Year: 2020 Title: Molecular mechanism of mitochondrial phosphatidate transfer by Ups1 Authors: Lu, J. / Chan, C. / Yu, L. / Fan, J. / Sun, F. / Zhai, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jql.cif.gz | 283.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jql.ent.gz | 235.4 KB | Display | PDB format |
PDBx/mmJSON format | 5jql.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jql_validation.pdf.gz | 510.6 KB | Display | wwPDB validaton report |
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Full document | 5jql_full_validation.pdf.gz | 522 KB | Display | |
Data in XML | 5jql_validation.xml.gz | 47.8 KB | Display | |
Data in CIF | 5jql_validation.cif.gz | 65.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jq/5jql ftp://data.pdbj.org/pub/pdb/validation_reports/jq/5jql | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21943.250 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: UPS1, YLR193C / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q05776 #2: Protein | Mass: 9723.954 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: MDM35, YKL053C-A / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O60200 #3: Protein | | Mass: 21990.145 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: UPS1, YLR193C / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q05776 #4: Protein | | Mass: 22037.039 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: UPS1, YLR193C / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q05776 #5: Protein | | Mass: 9770.850 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: MDM35, YKL053C-A / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O60200 |
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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: 2.35 Å3/Da / Density % sol: 47.72 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 8% Tacsimate, pH5.0, 20% PEG 3350, 200mM Sodium thiocyanate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 19, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.9→50 Å / Num. obs: 76995 / % possible obs: 98.4 % / Redundancy: 3.6 % / Biso Wilson estimate: 70.36 Å2 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.045 / Rrim(I) all: 0.087 / Χ2: 2.797 / Net I/av σ(I): 31.707 / Net I/σ(I): 14.9 / Num. measured all: 279505 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.9→48.404 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.51 Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 168.67 Å2 / Biso mean: 38.11 Å2 / Biso min: 0.13 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.9→48.404 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27
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