+Open data
-Basic information
Entry | Database: PDB / ID: 5y83 | ||||||
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Title | Crystal structure of YidC from Thermotoga maritima | ||||||
Components | Membrane protein insertase YidCBiological membrane | ||||||
Keywords | TRANSPORT PROTEIN / yidc / alb3 / oxa1 / sec | ||||||
Function / homology | Function and homology information membrane insertase activity / protein insertion into membrane / protein transport / plasma membrane Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.842 Å | ||||||
Authors | Huang, Y. / Xin, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: FASEB J. / Year: 2018 Title: Structure of YidC from Thermotoga maritima and its implications for YidC-mediated membrane protein insertion Authors: Xin, Y. / Zhao, Y. / Zheng, J. / Zhou, H. / Zhang, X.C. / Tian, C. / Huang, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5y83.cif.gz | 149.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5y83.ent.gz | 117.4 KB | Display | PDB format |
PDBx/mmJSON format | 5y83.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y8/5y83 ftp://data.pdbj.org/pub/pdb/validation_reports/y8/5y83 | HTTPS FTP |
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-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: 52261.875 Da / Num. of mol.: 1 / Mutation: T24V, K25V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria) Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: yidC, TM_1461 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9X1H2 |
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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: 4.87 Å3/Da / Density % sol: 81.04 % |
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Crystal grow | Temperature: 289 K / Method: evaporation / pH: 7.5 / Details: 0.1M HEPES (pH 7.5), 20% PEG1500(w/v) |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 8, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.8→50 Å / Num. obs: 10459 / % possible obs: 99.7 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.054 / Rrim(I) all: 0.128 / Χ2: 1.048 / Net I/σ(I): 4.4 / Num. measured all: 85442 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.842→42.758 Å / SU ML: 0.59 / Cross valid method: FREE R-VALUE / σ(F): 1.04 / Phase error: 32.91 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||
Displacement parameters | Biso max: 235.72 Å2 / Biso mean: 69.7552 Å2 / Biso min: 7.59 Å2 | ||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.842→42.758 Å
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