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Yorodumi- PDB-5vkz: Crystal structure of Mdm12 and combinatorial reconstitution of Md... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vkz | ||||||
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Title | Crystal structure of Mdm12 and combinatorial reconstitution of Mdm12/Mmm1 ERMES complexes for structural studies | ||||||
Components | Mitochondrial distribution and morphology protein 12 | ||||||
Keywords | LIPID TRANSPORT / MDM12 / ERMES COMPLEX / SMP DOMAIN | ||||||
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 | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.1 Å | ||||||
Authors | Egea, P.F. / AhYoung, A.P. / Lu, B. / Tan, H.R. / Cascio, D. | ||||||
Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2017 Title: Crystal structure of Mdm12 and combinatorial reconstitution of Mdm12/Mmm1 ERMES complexes for structural studies. Authors: AhYoung, A.P. / Lu, B. / Cascio, D. / Egea, P.F. #1: Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2015 Title: Conserved SMP domains of the ERMES complex bind phospholipids and mediate tether assembly. Authors: AhYoung, A.P. / Jiang, J. / Zhang, J. / Khoi Dang, X. / Loo, J.A. / Zhou, Z.H. / Egea, P.F. #2: Journal: EMBO Rep. / Year: 2016 Title: Crystal structure of Mdm12 reveals the architecture and dynamic organization of the ERMES complex. Authors: Jeong, H. / Park, J. / Lee, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vkz.cif.gz | 99.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vkz.ent.gz | 76.4 KB | Display | PDB format |
PDBx/mmJSON format | 5vkz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5vkz_validation.pdf.gz | 416.4 KB | Display | wwPDB validaton report |
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Full document | 5vkz_full_validation.pdf.gz | 422.7 KB | Display | |
Data in XML | 5vkz_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | 5vkz_validation.cif.gz | 15.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vk/5vkz ftp://data.pdbj.org/pub/pdb/validation_reports/vk/5vkz | HTTPS FTP |
-Related structure data
Related structure data | 5gydS S: Starting model for refinement |
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Similar 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 15 - 263 / Label seq-ID: 15 - 263
NCS ensembles :
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-Components
#1: Protein | Mass: 31222.145 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: AWRI1631 / Gene: MDM12, AWRI1631_151520 / Plasmid: pCDF / Details (production host): PLASMID / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: B5VRP4 |
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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: 5.11 Å3/Da / Density % sol: 75.91 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 15-25% PEG 3350, 400 mM ammonium phosphate, 3.5 mM Mega-10 PH range: 5.0-6.0 |
-Data collection
Diffraction | Mean temperature: 83 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 23, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 4.1→85.3 Å / Num. obs: 10272 / % possible obs: 99.5 % / Redundancy: 7.4 % / Biso Wilson estimate: 143.06 Å2 / Rmerge(I) obs: 0.115 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 4.1→4.21 Å / Redundancy: 7.5 % / Rmerge(I) obs: 1.05 / Mean I/σ(I) obs: 2 / Num. unique obs: 744 / CC1/2: 0.958 / Rsym value: 0.981 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5GYD Resolution: 4.1→85.34 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.945 / SU B: 49.37 / SU ML: 0.547 / Cross valid method: THROUGHOUT / ESU R Free: 0.658 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 1.1 Å / Shrinkage radii: 1.1 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 263.699 Å2
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Refinement step | Cycle: 1 / Resolution: 4.1→85.34 Å
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Refine LS restraints |
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