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Yorodumi- PDB-2zws: Crystal Structure Analysis of neutral ceramidase from Pseudomonas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zws | ||||||
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Title | Crystal Structure Analysis of neutral ceramidase from Pseudomonas aeruginosa | ||||||
Components | Neutral ceramidase | ||||||
Keywords | HYDROLASE / prism fold and beta-sandwich fold / Lipid metabolism / Secreted | ||||||
Function / homology | Function and homology information sphingosine catabolic process / ceramidase / N-acylsphingosine amidohydrolase activity / ceramidase activity / ceramide catabolic process / sphingosine biosynthetic process / long-chain fatty acid biosynthetic process / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Kakuta, Y. / Okino, N. / Inoue, T. / Okano, H. / Ito, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Mechanistic insights into the hydrolysis and synthesis of ceramide by neutral ceramidase. Authors: Inoue, T. / Okino, N. / Kakuta, Y. / Hijikata, A. / Okano, H. / Goda, H.M. / Tani, M. / Sueyoshi, N. / Kambayashi, K. / Matsumura, H. / Kai, Y. / Ito, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zws.cif.gz | 295.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zws.ent.gz | 247.7 KB | Display | PDB format |
PDBx/mmJSON format | 2zws.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zws_validation.pdf.gz | 665.3 KB | Display | wwPDB validaton report |
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Full document | 2zws_full_validation.pdf.gz | 690.1 KB | Display | |
Data in XML | 2zws_validation.xml.gz | 35.1 KB | Display | |
Data in CIF | 2zws_validation.cif.gz | 53.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zw/2zws ftp://data.pdbj.org/pub/pdb/validation_reports/zw/2zws | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 70855.266 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I596, ceramidase |
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-Non-polymers , 6 types, 676 molecules
#2: Chemical | ChemComp-ZN / | ||||||
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#3: Chemical | ChemComp-MG / | ||||||
#4: Chemical | #5: Chemical | ChemComp-PLM / | #6: Chemical | ChemComp-GOL / #7: Water | ChemComp-HOH / | |
-Details
Sequence details | THESE SEQUENCE ARE FROM REFERENCE 1 IN UNP DATABASE, Q9I596. |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.48 % |
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Crystal grow | Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. all: 131655 / Num. obs: 131655 / % possible obs: 90.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / Net I/σ(I): 17 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.621 / Mean I/σ(I) obs: 1.2 / Rsym value: 0.621 / % possible all: 51.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→22.6 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.544 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.075 / ESU R Free: 0.067 / 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: 20.951 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→22.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.401→1.437 Å / Total num. of bins used: 20
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