+Open data
-Basic information
Entry | Database: PDB / ID: 4by8 | ||||||
---|---|---|---|---|---|---|---|
Title | Microheterogeneous Paracelsin-X from Trichoderma reesei | ||||||
Components | PARACELSIN-X | ||||||
Keywords | ANTIBIOTIC / PEPTAIBOL / PEPTAIBIOTIC / MEMBRANE ACTIVE / PEPTIDE ANTIBIOTIC | ||||||
Function / homology | METHANOL / : Function and homology information | ||||||
Biological species | TRICHODERMA REESEI (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / DIRECT METHODS / Resolution: 0.94 Å | ||||||
Authors | Gessmann, R. / Petratos, K. | ||||||
Citation | Journal: To be Published Title: Microheterogeneous Paracelsin-X from Trichoderma Reesei Authors: Gessmann, R. / Petratos, K. | ||||||
History |
| ||||||
Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4by8.cif.gz | 19.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4by8.ent.gz | 15.5 KB | Display | PDB format |
PDBx/mmJSON format | 4by8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4by8_validation.pdf.gz | 439.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4by8_full_validation.pdf.gz | 440.4 KB | Display | |
Data in XML | 4by8_validation.xml.gz | 3.7 KB | Display | |
Data in CIF | 4by8_validation.cif.gz | 4.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/by/4by8 ftp://data.pdbj.org/pub/pdb/validation_reports/by/4by8 | HTTPS FTP |
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein/peptide | Mass: 1907.262 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) TRICHODERMA REESEI (fungus) / Strain: QM9414 / References: NOR: NOR01025 |
---|---|
#2: Chemical | ChemComp-MOH / |
#3: Water | ChemComp-HOH / |
Sequence details | THE PEPTIDE CRYSTALLIZED IS MICROHETEROGENEIC IN 4 POSITIONS IN THE SEQUENCE. ALA4 IS ALSO AIB4, ...THE PEPTIDE CRYSTALLIZ |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.55 Å3/Da / Density % sol: 20.47 % / Description: NONE |
---|---|
Crystal grow | Temperature: 294 K / Method: evaporation / Details: SLOW EVAPORATION AT ROOM TEMPERATURE |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 6, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8729 Å / Relative weight: 1 |
Reflection | Resolution: 0.94→11.31 Å / Num. obs: 7699 / % possible obs: 98.4 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 0.94→0.99 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: DIRECT METHODS Starting model: NONE Resolution: 0.94→11.31 Å / Num. parameters: 1305 / Num. restraintsaints: 1321 / Cross valid method: THROUGHOUT / σ(F): 0
| |||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: MOEWS,KRETSINGER | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 4 / Occupancy sum hydrogen: 147 / Occupancy sum non hydrogen: 139.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.94→11.31 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
|