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Yorodumi- PDB-1yf5: Cyto-Epsl: The Cytoplasmic Domain Of Epsl, An Inner Membrane Comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yf5 | ||||||
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Title | Cyto-Epsl: The Cytoplasmic Domain Of Epsl, An Inner Membrane Component Of The Type II Secretion System Of Vibrio Cholerae | ||||||
Components | General secretion pathway protein L | ||||||
Keywords | TRANSPORT PROTEIN / Type II secretion / secretory protein | ||||||
Function / homology | Function and homology information Gram-negative-bacterium-type cell wall / protein secretion by the type II secretion system / type II protein secretion system complex / plasma membrane Similarity search - Function | ||||||
Biological species | Vibrio cholerae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Abendroth, J. / Murphy, P. / Mushtaq, A. / Sandkvist, M. / Bagdasarian, M. / Hol, W.G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: The X-ray Structure of the Type II Secretion System Complex Formed by the N-terminal Domain of EpsE and the Cytoplasmic Domain of EpsL of Vibrio cholerae. Authors: Abendroth, J. / Murphy, P. / Sandkvist, M. / Bagdasarian, M. / Hol, W.G. #1: Journal: J.Mol.Biol. / Year: 2004 Title: The Structure of the Cytoplasmic Domain of Epsl, an Inner Membrane Component of the Type II Secretio System of Vibrio Cholerae: An Unusual Member of the Actin-Like ATPase Superfamily Authors: Abendroth, J. / Bagdasarian, M. / Sandkvist, M. / Hol, W.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yf5.cif.gz | 59.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yf5.ent.gz | 42.8 KB | Display | PDB format |
PDBx/mmJSON format | 1yf5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yf5_validation.pdf.gz | 425.6 KB | Display | wwPDB validaton report |
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Full document | 1yf5_full_validation.pdf.gz | 428.6 KB | Display | |
Data in XML | 1yf5_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | 1yf5_validation.cif.gz | 13.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yf/1yf5 ftp://data.pdbj.org/pub/pdb/validation_reports/yf/1yf5 | HTTPS FTP |
-Related structure data
Related structure data | 2bh1C 1w97S 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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Unit cell |
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Details | the second half of the dimer is generated by the crystallographic two-fold: -x+2, y, -z |
-Components
#1: Protein | Mass: 28528.854 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: epsL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21gold(DE3) / References: UniProt: P45782 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 51.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 15% PEG 6000, 150mM calcium acetate, 100mM tris pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97951 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 29, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97951 Å / Relative weight: 1 |
Reflection | Resolution: 2.74→20 Å / Num. all: 7122 / Num. obs: 7122 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 87.4 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2.74→2.8 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.4 / Rsym value: 0.37 / % possible all: 81 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1w97 Resolution: 2.75→20 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.919 / SU B: 42.646 / SU ML: 0.35 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.402 / 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: 76.835 Å2
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Refinement step | Cycle: LAST / Resolution: 2.75→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.75→2.896 Å / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Origin x: 45.6585 Å / Origin y: -4.0897 Å / Origin z: 12.534 Å
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Refinement TLS group |
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