+Open data
-Basic information
Entry | Database: PDB / ID: 5yk6 | ||||||
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Title | Crystal Structure of Mmm1 | ||||||
Components | Maintenance of mitochondrial morphology protein 1 | ||||||
Keywords | LIPID TRANSPORT / ERMES / Phospholipid / Membrane contact site | ||||||
Function / homology | Function and homology information ERMES complex / mitochondrial genome maintenance / lipid transport / protein insertion into mitochondrial outer membrane / lipid binding / endoplasmic reticulum membrane Similarity search - Function | ||||||
Biological species | Zygosaccharomyces rouxii (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å | ||||||
Authors | Jeong, H. / Park, J. / Lee, C. | ||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017 Title: Crystal structures of Mmm1 and Mdm12-Mmm1 reveal mechanistic insight into phospholipid trafficking at ER-mitochondria contact sites. Authors: Jeong, H. / Park, J. / Jun, Y. / Lee, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yk6.cif.gz | 118.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yk6.ent.gz | 91.2 KB | Display | PDB format |
PDBx/mmJSON format | 5yk6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5yk6_validation.pdf.gz | 911 KB | Display | wwPDB validaton report |
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Full document | 5yk6_full_validation.pdf.gz | 919.1 KB | Display | |
Data in XML | 5yk6_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | 5yk6_validation.cif.gz | 15.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yk/5yk6 ftp://data.pdbj.org/pub/pdb/validation_reports/yk/5yk6 | 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: 29583.342 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zygosaccharomyces rouxii (strain ATCC 2623 / CBS 732 / NBRC 1130 / NCYC 568 / NRRL Y-229) (yeast) Strain: ATCC 2623 / CBS 732 / NBRC 1130 / NCYC 568 / NRRL Y-229 Gene: MMM1, ZYRO0B10274g / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C5DRQ1 | ||
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#2: Chemical | #3: 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: 4.68 Å3/Da / Density % sol: 73.71 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG 10000, HEPES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 13895 / % possible obs: 99.2 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 26.8 |
Reflection shell | Resolution: 2.8→2.85 Å |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.8→41.081 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 24.79
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→41.081 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 49.1436 Å / Origin y: -14.7777 Å / Origin z: 64.2078 Å
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Refinement TLS group | Selection details: (chain 'A' and resid 194 through 439) |