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Yorodumi- PDB-5n7l: Crystal structure of the periplasmic domain of XcpY, tI crystal form. -
+Open data
-Basic information
Entry | Database: PDB / ID: 5n7l | ||||||
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Title | Crystal structure of the periplasmic domain of XcpY, tI crystal form. | ||||||
Components | Type II secretion system protein L | ||||||
Keywords | PROTEIN TRANSPORT / periplasm / ferrodoxin fold / GspL 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 | Pseudomonas aeruginosa PAO1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.501 Å | ||||||
Authors | Fulara, A. / Savvides, S.N. | ||||||
Citation | Journal: Sci Rep / Year: 2018 Title: Structure and oligomerization of the periplasmic domain of GspL from the type II secretion system of Pseudomonas aeruginosa. Authors: Fulara, A. / Vandenberghe, I. / Read, R.J. / Devreese, B. / Savvides, S.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5n7l.cif.gz | 44.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5n7l.ent.gz | 31.2 KB | Display | PDB format |
PDBx/mmJSON format | 5n7l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5n7l_validation.pdf.gz | 433.1 KB | Display | wwPDB validaton report |
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Full document | 5n7l_full_validation.pdf.gz | 433.2 KB | Display | |
Data in XML | 5n7l_validation.xml.gz | 5.5 KB | Display | |
Data in CIF | 5n7l_validation.cif.gz | 6.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n7/5n7l ftp://data.pdbj.org/pub/pdb/validation_reports/n7/5n7l | HTTPS FTP |
-Related structure data
Related structure data | 6ghuC 5n7s 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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 8112.118 Da / Num. of mol.: 1 / Fragment: periplasmic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: xcpY, PA3096 / Plasmid: pRSF 1b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P25060 | ||||
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#2: Chemical | #3: Chemical | #4: 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: 6.23 Å3/Da / Density % sol: 80.25 % / Description: bipiramide |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.3 M KBr or 0.2 M MgCl2, 0.1 M sodium cacodylate, pH=6.5, gamma-PGA |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 31, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→41 Å / Num. obs: 9039 / % possible obs: 99.7 % / Redundancy: 12.97 % / Rrim(I) all: 0.13 / Net I/σ(I): 16.56 |
Reflection shell | Resolution: 2.5→2.65 Å / Redundancy: 12.02 % / Num. unique obs: 1419 / % possible all: 98.5 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5N7S 5n7s Resolution: 2.501→40.894 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.7
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 168.83 Å2 / Biso mean: 75.5813 Å2 / Biso min: 39.5 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.501→40.894 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6
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Refinement TLS params. | Method: refined / Origin x: 15.5543 Å / Origin y: -0.0021 Å / Origin z: -5.7139 Å
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Refinement TLS group |
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