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Yorodumi- PDB-6y86: Active YidC insertase crystal structure with the first transmembr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6y86 | ||||||
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Title | Active YidC insertase crystal structure with the first transmembrane domain resolved | ||||||
Components | Membrane protein insertase YidCBiological membrane | ||||||
Keywords | MEMBRANE PROTEIN / Insertase and chaperone | ||||||
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: 3.4 Å | ||||||
Authors | Li, X.D. / Nass, K. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: Biochim Biophys Acta Biomembr / Year: 2022 Title: The role of the N-terminal amphipathic helix in bacterial YidC: Insights from functional studies, the crystal structure and molecular dynamics simulations. Authors: Nass, K.J. / Ilie, I.M. / Saller, M.J. / Driessen, A.J.M. / Caflisch, A. / Kammerer, R.A. / Li, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6y86.cif.gz | 187.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6y86.ent.gz | 157.4 KB | Display | PDB format |
PDBx/mmJSON format | 6y86.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y8/6y86 ftp://data.pdbj.org/pub/pdb/validation_reports/y8/6y86 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 49201.246 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria) Gene: yidC, TM_1461 / Production host: Escherichia coli (E. coli) / 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: 3.71 Å3/Da / Density % sol: 66.82 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.1M Bis-Tris, pH5.5, 0.2M di-ammonium hydrogen citrate with 24% PEG 3350. PH range: 4.6-5.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 X 1M / Detector: PIXEL / Date: Oct 30, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→48.55 Å / Num. obs: 10680 / % possible obs: 100 % / Redundancy: 30.1 % / CC1/2: 1 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 3.4→20 Å / Num. unique obs: 10052 / CC1/2: 1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: experiment Resolution: 3.4→19.994 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 35.43
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 405.26 Å2 / Biso mean: 156.3716 Å2 / Biso min: 64.29 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.4→19.994 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Origin x: -18.1047 Å / Origin y: -10.5926 Å / Origin z: -24.1688 Å
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Refinement TLS group | Selection details: all |