+Open data
-Basic information
Entry | Database: PDB / ID: 6i1m | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Secreted type 1 cystatin from Fasciola hepatica | ||||||||||||
Components | Cystatin | ||||||||||||
Keywords | Hydrolase inhibitor / cystatin / stefin / protease inhibitor / fasciola hepatica | ||||||||||||
Function / homology | IODIDE ION / Type-1 cystatin cysteine protease inhibitor / Cystatin Function and homology information | ||||||||||||
Biological species | Fasciola hepatica (liver fluke) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.6 Å | ||||||||||||
Authors | Busa, M. / Rezacova, P. / Pachl, P. / Stefanic, S. / Mares, M. | ||||||||||||
Funding support | Czech Republic, 3items
| ||||||||||||
Citation | Journal: J.Biol.Chem. / Year: 2023 Title: An evolutionary molecular adaptation of an unusual stefin from the liver fluke Fasciola hepatica redefines the cystatin superfamily. Authors: Busa, M. / Matouskova, Z. / Bartosova-Sojkova, P. / Pachl, P. / Rezacova, P. / Eichenberger, R.M. / Deplazes, P. / Horn, M. / Stefanic, S. / Mares, M. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6i1m.cif.gz | 30.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6i1m.ent.gz | 21.3 KB | Display | PDB format |
PDBx/mmJSON format | 6i1m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6i1m_validation.pdf.gz | 412.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6i1m_full_validation.pdf.gz | 412.9 KB | Display | |
Data in XML | 6i1m_validation.xml.gz | 6.9 KB | Display | |
Data in CIF | 6i1m_validation.cif.gz | 8.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i1/6i1m ftp://data.pdbj.org/pub/pdb/validation_reports/i1/6i1m | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 9799.197 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: IRG: N-terminal cloning artifact AAAHHHHHH: C-terminal His-tag E36V, I54T: natural mutations found in the sequence (compared to GenBank AAV68752.1) Source: (gene. exp.) Fasciola hepatica (liver fluke) / Gene: Cyt / Production host: Komagataella phaffii GS115 (fungus) / References: UniProt: Q17TZ2, UniProt: A0A2H1BUS1*PLUS | ||
---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.43 % / Description: very small needles in phase separation |
---|---|
Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2.0M Ammonium Sulfate 0.1M Sodium Iodide 0.1M Sodium HEPES 7.5 5% v/v PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184, 1.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 29, 2018 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6→46.67 Å / Num. obs: 13043 / % possible obs: 98.4 % / Redundancy: 6.717 % / Biso Wilson estimate: 26.772 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.158 / Rrim(I) all: 0.172 / Χ2: 1.17 / Net I/σ(I): 7.94 / Num. measured all: 87605 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SIRAS / Resolution: 1.6→46.67 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 max: 74.33 Å2 / Biso mean: 26.132 Å2 / Biso min: 16.61 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.6→46.67 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.597→1.639 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|