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Open data
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Basic information
Entry | Database: PDB / ID: 5ch4 | ||||||
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Title | Peptide-Bound State of Thermus thermophilus SecYEG | ||||||
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![]() | PROTEIN TRANSPORT / translocon / membrane protein | ||||||
Function / homology | ![]() cell envelope Sec protein transport complex / protein transport by the Sec complex / intracellular protein transmembrane transport / protein-transporting ATPase activity / signal sequence binding / SRP-dependent cotranslational protein targeting to membrane, translocation / protein secretion / protein transmembrane transporter activity / protein targeting / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tanaka, Y. / Sugano, Y. / Takemoto, M. / Kusakizako, T. / Kumazaki, K. / Ishitani, R. / Nureki, O. / Tsukazaki, T. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 117.6 KB | Display | ![]() |
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PDB format | ![]() | 90.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.2 KB | Display | ![]() |
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Full document | ![]() | 448.6 KB | Display | |
Data in XML | ![]() | 20.2 KB | Display | |
Data in CIF | ![]() | 26.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5awwC ![]() 2zjsS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() Strain: HB8 / ATCC 27634 / DSM 579 / Gene: secY, TTHA1672 Production host: ![]() ![]() 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.) ![]() ![]() Strain: HB8 / ATCC 27634 / DSM 579 / Gene: secE, TTHA0249 Production host: ![]() ![]() 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.) ![]() ![]() Strain: HB8 / ATCC 27634 / DSM 579 / Gene: TTHA1784 Production host: ![]() ![]() References: UniProt: Q5SHE6 |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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