[English] 日本語
Yorodumi- PDB-5v3s: Crystal structure of IP-1A from Alcaligenes faecalis at 1.8A reso... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5v3s | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of IP-1A from Alcaligenes faecalis at 1.8A resolution | ||||||
Components | Two-component insecticidal protein 16 kDa unit | ||||||
Keywords | TOXIN / insecticidal toxin / Aegerolysin | ||||||
Function / homology | Mutm (Fpg) Protein; Chain: A, domain 2 - #50 / Hemolysin, aegerolysin type / Aegerolysin / Mutm (Fpg) Protein; Chain: A, domain 2 / hemolysis by symbiont of host erythrocytes / Sandwich / Mainly Beta / Two-component insecticidal protein 16 kDa unit Function and homology information | ||||||
Biological species | Alcaligenes faecalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Yalpani, N. / Altier, D. / Guan, R. / Montelione, G. | ||||||
Citation | Journal: Sci Rep / Year: 2017 Title: An Alcaligenes strain emulates Bacillus thuringiensis producing a binary protein that kills corn rootworm through a mechanism similar to Cry34Ab1/Cry35Ab1. Authors: Yalpani, N. / Altier, D. / Barry, J. / Kassa, A. / Nowatzki, T.M. / Sethi, A. / Zhao, J.Z. / Diehn, S. / Crane, V. / Sandahl, G. / Guan, R. / Poland, B. / Perez Ortega, C. / Nelson, M.E. / ...Authors: Yalpani, N. / Altier, D. / Barry, J. / Kassa, A. / Nowatzki, T.M. / Sethi, A. / Zhao, J.Z. / Diehn, S. / Crane, V. / Sandahl, G. / Guan, R. / Poland, B. / Perez Ortega, C. / Nelson, M.E. / Xie, W. / Liu, L. / Wu, G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5v3s.cif.gz | 70.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5v3s.ent.gz | 57.1 KB | Display | PDB format |
PDBx/mmJSON format | 5v3s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5v3s_validation.pdf.gz | 440.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5v3s_full_validation.pdf.gz | 445.7 KB | Display | |
Data in XML | 5v3s_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 5v3s_validation.cif.gz | 23.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v3/5v3s ftp://data.pdbj.org/pub/pdb/validation_reports/v3/5v3s | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 17375.842 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alcaligenes faecalis (bacteria) / Gene: IP-1A / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0U4HUZ5 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.13 % |
---|---|
Crystal grow | Temperature: 295 K / Method: microbatch / pH: 7 Details: 0.1M HEPES, pH=7.0 10% PEG 1000 0.1M Sodium Malonate |
-Data collection
Diffraction | Mean temperature: 80 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97869 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jan 19, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97869 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→40 Å / Num. obs: 26255 / % possible obs: 97.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 14.81 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 1.8→27.99 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.91 / SU B: 3.313 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 23.473 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.8→27.99 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|