+Open data
-Basic information
Entry | Database: PDB / ID: 4xhr | ||||||
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Title | Structure of a phospholipid trafficking complex, native | ||||||
Components |
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Keywords | LIPID TRANSPORT/OXIDOREDUCTASE / phospholipid / LIPID TRANSPORT-OXIDOREDUCTASE complex | ||||||
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: 2.55 Å | ||||||
Authors | Yu, F. / He, F. / Wang, C. / Zhang, P. | ||||||
Citation | Journal: Embo Rep. / Year: 2015 Title: Structural basis of intramitochondrial phosphatidic acid transport mediated by Ups1-Mdm35 complex Authors: Yu, F. / He, F. / Yao, H. / Wang, C. / Wang, J. / Li, J. / Qi, X. / Xue, H. / Ding, J. / Zhang, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xhr.cif.gz | 201.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xhr.ent.gz | 170.4 KB | Display | PDB format |
PDBx/mmJSON format | 4xhr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xh/4xhr ftp://data.pdbj.org/pub/pdb/validation_reports/xh/4xhr | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 21755.670 Da / Num. of mol.: 2 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 (E. coli) / References: UniProt: Q05776 #2: Protein | Mass: 9723.954 Da / Num. of mol.: 2 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 (E. coli) / References: UniProt: O60200 #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.78 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop Details: 2%(v/v) Tacsimate pH 6.0, 0.1M Bis-Tris pH 6.5, 20%(w/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.7 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 8, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.7 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→32.08 Å / Num. obs: 17640 / % possible obs: 97.17 % / Redundancy: 3.5 % / Net I/σ(I): 11.96 |
Reflection shell | Resolution: 2.55→3 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.116 / Mean I/σ(I) obs: 11.96 / % possible all: 97.17 |
-Processing
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Refinement | Method to determine structure: SAD / Resolution: 2.55→32.08 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.891 / SU B: 25.837 / SU ML: 0.26 / Cross valid method: THROUGHOUT / ESU R: 1.232 / ESU R Free: 0.353 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 78.621 Å2
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Refinement step | Cycle: LAST / Resolution: 2.55→32.08 Å
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