+Open data
-Basic information
Entry | Database: PDB / ID: 5zu4 | ||||||
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Title | Crystal structure of Lamprey immune protein | ||||||
Components | Natterin-like protein | ||||||
Keywords | ANTITUMOR PROTEIN / lamprey / pore-forming protein / cytotoxin | ||||||
Function / homology | Aerolysin-like toxin / Clostridium epsilon toxin ETX/Bacillus mosquitocidal toxin MTX2 / Jacalin-like lectin domain / Jacalin-type lectin domain profile. / Jacalin-like lectin domain superfamily / DI(HYDROXYETHYL)ETHER / Natterin-like protein Function and homology information | ||||||
Biological species | Lethenteron camtschaticum (Arctic lamprey) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å | ||||||
Authors | Li, Q.W. / Pang, Y. | ||||||
Citation | Journal: To Be Published Title: Structure of a pore-forming protein Authors: Li, Q.W. / Pang, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zu4.cif.gz | 137.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zu4.ent.gz | 106 KB | Display | PDB format |
PDBx/mmJSON format | 5zu4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zu/5zu4 ftp://data.pdbj.org/pub/pdb/validation_reports/zu/5zu4 | HTTPS FTP |
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-Related structure data
Related structure data | 6iulC 4nzoS 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 34340.805 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lethenteron camtschaticum (Arctic lamprey) Production host: Escherichia coli (E. coli) / References: UniProt: K7WEH5 |
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-Non-polymers , 5 types, 157 molecules
#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-PEG / | #6: 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: 3.38 Å3/Da / Density % sol: 63.56 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 1,4-Dioxane, Polyethylene glycol 20000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9798 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 20, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→89.08 Å / Num. obs: 41118 / % possible obs: 99.9 % / Redundancy: 16 % / Net I/σ(I): 28.3 |
Reflection shell | Resolution: 2.25→2.29 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4NZO Resolution: 2.39→89.08 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.923 / SU B: 7.38 / SU ML: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.267 / ESU R Free: 0.227 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 164.27 Å2 / Biso mean: 52.299 Å2 / Biso min: 25.98 Å2
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Refinement step | Cycle: final / Resolution: 2.39→89.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.389→2.451 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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