[English] 日本語
Yorodumi- PDB-7bwx: Crystal structure of ice-binding protein from an Antarctic ascomy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bwx | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of ice-binding protein from an Antarctic ascomycete, Antarctomyces psychrotrophicus. | |||||||||
Components | Ice-binding protein isoform1a | |||||||||
Keywords | ANTIFREEZE PROTEIN / BETA-SOLENOID / RIGHT-HANDED BETA-HELIX | |||||||||
Function / homology | Ice-binding protein / Ice-binding-like / Ice-binding protein isoform1a Function and homology information | |||||||||
Biological species | Antarctomyces psychrotrophicus (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.904 Å | |||||||||
Authors | Yamauchi, A. / Arai, T. / Kondo, H. / Tsuda, S. | |||||||||
Funding support | Japan, 2items
| |||||||||
Citation | Journal: Biomolecules / Year: 2020 Title: An Ice-Binding Protein from an Antarctic Ascomycete Is Fine-Tuned to Bind to Specific Water Molecules Located in the Ice Prism Planes. Authors: Yamauchi, A. / Arai, T. / Kondo, H. / Sasaki, Y.C. / Tsuda, S. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7bwx.cif.gz | 266.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7bwx.ent.gz | 204.8 KB | Display | PDB format |
PDBx/mmJSON format | 7bwx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7bwx_validation.pdf.gz | 489.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7bwx_full_validation.pdf.gz | 494.2 KB | Display | |
Data in XML | 7bwx_validation.xml.gz | 59 KB | Display | |
Data in CIF | 7bwx_validation.cif.gz | 90.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bw/7bwx ftp://data.pdbj.org/pub/pdb/validation_reports/bw/7bwx | HTTPS FTP |
-Related structure data
Related structure data | 7bwyC 3wp9S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
5 |
| ||||||||
6 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 22276.666 Da / Num. of mol.: 6 / Mutation: N55D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Antarctomyces psychrotrophicus (fungus) Gene: ibp / Production host: Komagataella pastoris (fungus) / References: UniProt: A0A2Z6DSM4 #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.38 Å3/Da / Density % sol: 64 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.6 Details: 0.1 M HEPES-NaOH pH 8.6, 0.95 M ammonium sulfate and 0.1 M lithium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→47.62 Å / Num. obs: 141990 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 15.45 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.045 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 1.9→2.01 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.467 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 20446 / CC1/2: 0.888 / Rpim(I) all: 0.197 / % possible all: 99.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WP9 Resolution: 1.904→47.62 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.002 / SU ML: 0.057 / Cross valid method: FREE R-VALUE / ESU R: 0.085 / ESU R Free: 0.087 Details: Hydrogens have been added in their riding positions
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.482 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.904→47.62 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|