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Yorodumi- PDB-4ps6: Crystal structure of an inhibitor of vertebrate lysozyme (PA3902)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ps6 | ||||||
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Title | Crystal structure of an inhibitor of vertebrate lysozyme (PA3902) from Pseudomonas aeruginosa PAO1 at 1.25 A resolution | ||||||
Components | Inhibitor of vertebrate lysozyme | ||||||
Keywords | TOXIN / PF08816 family / Ivy / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY | ||||||
Function / homology | Inhibitor of vertebrate lysozyme / Inhibitor of vertebrate lysozyme / Inhibitor of vertebrate lysozyme superfamily / Inhibitor of vertebrate lysozyme (Ivy) / Inhibitor of vertebrate lysozyme, Ivy / periplasmic space / 3-Layer(aba) Sandwich / Alpha Beta / Inhibitor of vertebrate lysozyme Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.25 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of an inhibitor of vertebrate lysozyme (PA3902) from Pseudomonas aeruginosa PAO1 at 1.25 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ps6.cif.gz | 75.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ps6.ent.gz | 58.4 KB | Display | PDB format |
PDBx/mmJSON format | 4ps6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ps/4ps6 ftp://data.pdbj.org/pub/pdb/validation_reports/ps/4ps6 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14675.914 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: ivy, PA3902 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q9HXB1 |
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#2: Water | ChemComp-HOH / |
Sequence details | THIS CONSTRUCT (RESIDUES 25-153) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 25-153) WAS EXPRESSED WITH A PURIFICATI |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.51 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.2M ammonium acetate, 30.0% polyethylene glycol 4000, 0.1M sodium acetate pH 4.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97959 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2013 Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: single crystal Si(111) bent / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97959 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.25→36.126 Å / Num. obs: 26432 / % possible obs: 84.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 9.938 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 15.57 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: SAD |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.25→36.126 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.97 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 1.605 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.05 / ESU R Free: 0.051 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3.EXPERIMENTAL PHASES IN THE FORM OF HL COEFFICIENTS WERE USED AS RESTRAINTS DURING CRYSTALLOGRAPHIC REFINEMENT.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 61.88 Å2 / Biso mean: 14.0087 Å2 / Biso min: 4.75 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→36.126 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.254→1.287 Å / Total num. of bins used: 20
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