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Yorodumi- PDB-2yxq: The plug domain of the SecY protein stablizes the closed state of... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yxq | ||||||
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Title | The plug domain of the SecY protein stablizes the closed state of the translocation channel and maintains a membrane seal | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / protein translocation / signal peptide / membrane protein / protein secretion / prl mutation | ||||||
Function / homology | Function and homology information intracellular protein transmembrane transport / SRP-dependent cotranslational protein targeting to membrane, translocation / signal sequence binding / protein transmembrane transporter activity / protein secretion / protein targeting / protein transport / plasma membrane Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | ||||||
Authors | Li, W. / Schulman, S. | ||||||
Citation | Journal: Mol.Cell / Year: 2007 Title: The plug domain of the SecY protein stabilizes the closed state of the translocation channel and maintains a membrane seal Authors: Li, W. / Schulman, S. / Boyd, D. / Erlandson, K. / Beckwith, J. / Rapoport, T.A. | ||||||
History |
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Remark 999 | SEQUENCE deletion of 60-65 and substitution with one Gly |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yxq.cif.gz | 106.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yxq.ent.gz | 82 KB | Display | PDB format |
PDBx/mmJSON format | 2yxq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yx/2yxq ftp://data.pdbj.org/pub/pdb/validation_reports/yx/2yxq | HTTPS FTP |
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-Related structure data
Related structure data | 2yxrC 1rhzS 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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3 |
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4 |
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Unit cell |
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Details | The biological assembly is a monomer in the asymmetric unit |
-Components
#1: Protein | Mass: 46938.301 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Gene: secY / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): C43 / References: UniProt: Q60175 |
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#2: Protein | Mass: 8451.144 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Gene: secE / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): C43 / References: UniProt: Q57817 |
#3: Protein | Mass: 5967.010 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Gene: secG / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): C43 / References: UniProt: P60460 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.82 Å3/Da / Density % sol: 74.51 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 40-55% PEG400, 50mM Glycine-HCl , pH9, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 11, 2006 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97921 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→50 Å / Num. all: 14806 / Num. obs: 14678 / % possible obs: 98.6 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 2.3 / Redundancy: 12 % / Biso Wilson estimate: 118.6 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 21.9 |
Reflection shell | Resolution: 3.5→3.63 Å / Redundancy: 12 % / Rmerge(I) obs: 0.787 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1419 / Rsym value: 0.787 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RHZ Resolution: 3.5→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.5 / σ(I): 2.3 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: -0.367 Å2
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Refinement step | Cycle: LAST / Resolution: 3.5→50 Å
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LS refinement shell |
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