+Open data
-Basic information
Entry | Database: PDB / ID: 2zqp | ||||||
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Title | Crystal Structure of SecYE translocon from Thermus thermophilus | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / TRANSLOCON / SEC / PROTEIN-CONDUCTING-CHANNEL / Membrane / Translocation / Transmembrane / Transport | ||||||
Function / homology | Function and homology information protein transport by the Sec complex / intracellular protein transmembrane transport / protein transmembrane transporter activity / protein secretion / protein targeting / plasma membrane Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6 Å | ||||||
Authors | Tsukazaki, T. / Nureki, O. | ||||||
Citation | Journal: Nature / Year: 2008 Title: Conformational transition of Sec machinery inferred from bacterial SecYE structures Authors: Tsukazaki, T. / Mori, H. / Fukai, S. / Ishitani, R. / Mori, T. / Dohmae, N. / Perederina, A. / Sugita, Y. / Vassylyev, D.G. / Ito, K. / Nureki, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zqp.cif.gz | 97.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zqp.ent.gz | 75.1 KB | Display | PDB format |
PDBx/mmJSON format | 2zqp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zq/2zqp ftp://data.pdbj.org/pub/pdb/validation_reports/zq/2zqp | HTTPS FTP |
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-Related structure data
Related structure data | 2zjsSC S: Starting model for refinement C: citing same article (ref.) |
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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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-Components
#1: Protein | Mass: 47643.102 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-434 / Mutation: L2V, R252G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: PTV118N / Production host: Escherichia coli (E. coli) / References: UniProt: Q8KZP3, UniProt: Q5SHQ8*PLUS |
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#2: Protein | Mass: 7072.410 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: PTV118N / Production host: Escherichia coli (E. coli) / References: UniProt: Q8KZP4, UniProt: P38383*PLUS |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.64 Å3/Da / Density % sol: 73.49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 28.5% PEG 3350, 0.18M Na-citrate, 0.015% octaethylene glycol monododecyl ether, 5% glycerol, 0.0001M Pefabloc, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 23, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 6→50 Å / Num. obs: 2743 / % possible obs: 93.4 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: the SecYE structure produced by MD simulation using 2ZJS structure Resolution: 6→42.92 Å / Cor.coef. Fo:Fc: 0.783 / Cor.coef. Fo:Fc free: 0.729 / SU B: 436.011 / SU ML: 4.28 / Cross valid method: THROUGHOUT / ESU R Free: 3.246 / 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: 368.097 Å2
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Refinement step | Cycle: LAST / Resolution: 6→42.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 5.998→6.153 Å / Total num. of bins used: 20
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