+Open data
-Basic information
Entry | Database: PDB / ID: 5ch4 | ||||||
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Title | Peptide-Bound State of Thermus thermophilus SecYEG | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / translocon / membrane protein | ||||||
Function / homology | Function and homology information protein transport by the Sec complex / intracellular protein transmembrane transport / protein-transporting ATPase activity / 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: 3.64 Å | ||||||
Authors | Tanaka, Y. / Sugano, Y. / Takemoto, M. / Kusakizako, T. / Kumazaki, K. / Ishitani, R. / Nureki, O. / Tsukazaki, T. | ||||||
Citation | Journal: Cell Rep / Year: 2015 Title: Crystal Structures of SecYEG in Lipidic Cubic Phase Elucidate a Precise Resting and a Peptide-Bound State. Authors: Tanaka, Y. / Sugano, Y. / Takemoto, M. / Mori, T. / Furukawa, A. / Kusakizako, T. / Kumazaki, K. / Kashima, A. / Ishitani, R. / Sugita, Y. / Nureki, O. / Tsukazaki, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ch4.cif.gz | 117.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ch4.ent.gz | 90.1 KB | Display | PDB format |
PDBx/mmJSON format | 5ch4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ch/5ch4 ftp://data.pdbj.org/pub/pdb/validation_reports/ch/5ch4 | HTTPS FTP |
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-Related structure data
Related structure data | 5awwC 2zjsS C: citing same article (ref.) 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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Unit cell |
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-Components
#1: Protein | Mass: 48515.910 Da / Num. of mol.: 1 / Mutation: L2V, K248G, V249A, V250A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / Gene: secY, TTHA1672 Production host: Escherichia coli BL21-Gold(DE3)pLysS AG (bacteria) References: UniProt: Q5SHQ8 |
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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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / Gene: secE, TTHA0249 Production host: Escherichia coli BL21-Gold(DE3)pLysS AG (bacteria) References: UniProt: P38383 |
#3: Protein | Mass: 7943.501 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 43-117 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / Gene: TTHA1784 Production host: Escherichia coli BL21-Gold(DE3)pLysS AG (bacteria) References: UniProt: Q5SHE6 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 60.17 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 7.5 / Details: PEG 500DME, ZnSO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jul 18, 2014 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.6→50 Å / Num. obs: 9099 / % possible obs: 99.8 % / Redundancy: 7.4 % / Net I/σ(I): 5.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ZJS Resolution: 3.64→44.393 Å / SU ML: 0.51 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 30.9 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.64→44.393 Å
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Refine LS restraints |
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LS refinement shell |
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