+Open data
-Basic information
Entry | Database: PDB / ID: 6a0n | |||||||||
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Title | The crystal structure of apo-Lpg2622 | |||||||||
Components | Lpg2622 | |||||||||
Keywords | HYDROLASE / Cysteine proteases | |||||||||
Function / homology | Papain-like cysteine peptidase superfamily / Uncharacterized protein Function and homology information | |||||||||
Biological species | Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | |||||||||
Authors | Gong, X. / Ge, H. | |||||||||
Funding support | China, 2items
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Citation | Journal: FEBS Lett. / Year: 2018 Title: Structural characterization of the hypothetical protein Lpg2622, a new member of the C1 family peptidases from Legionella pneumophila Authors: Gong, X. / Zhao, X. / Zhang, W. / Wang, J. / Chen, X. / Hameed, M.F. / Zhang, N. / Ge, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6a0n.cif.gz | 137 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6a0n.ent.gz | 112.1 KB | Display | PDB format |
PDBx/mmJSON format | 6a0n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6a0n_validation.pdf.gz | 439.6 KB | Display | wwPDB validaton report |
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Full document | 6a0n_full_validation.pdf.gz | 447.1 KB | Display | |
Data in XML | 6a0n_validation.xml.gz | 25.8 KB | Display | |
Data in CIF | 6a0n_validation.cif.gz | 36.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/6a0n ftp://data.pdbj.org/pub/pdb/validation_reports/a0/6a0n | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 38081.855 Da / Num. of mol.: 2 / Fragment: UNP residues 20-353 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria) Strain: Philadelphia 1 / Gene: lpg2622 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZS97 #2: Water | ChemComp-HOH / | |
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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: 3.42 Å3/Da / Density % sol: 64.06 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / Details: 0.4M Sodium acetate trihydrate, pH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97916 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 20, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97916 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 59115 / % possible obs: 100 % / Redundancy: 16.9 % / Net I/σ(I): 24.8 |
Reflection shell | Resolution: 2.1→2.14 Å |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.481 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.148 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.646 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→50 Å
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Refine LS restraints |
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