+Open data
-Basic information
Entry | Database: PDB / ID: 1ob6 | ||||||
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Title | Cephaibol B | ||||||
Components | CEPHAIBOL B | ||||||
Keywords | ANTIBIOTIC / CEPHAIBOL / PEPTAIBOL / ANTIBACTERIAL / ANTIFUNGAL / ION CHANNEL | ||||||
Function / homology | Cephaibol B / ACETATE ION / ETHANOL / : Function and homology information | ||||||
Biological species | ACREMONIUM TUBAKII (fungus) | ||||||
Method | X-RAY DIFFRACTION / DIRECT METHODS / Resolution: 0.89 Å | ||||||
Authors | Bunkoczi, G. / Schiell, M. / Vertesy, L. / Sheldrick, G.M. | ||||||
Citation | Journal: J.Pept.Sci. / Year: 2003 Title: Crystal Structures of Cephaibols Authors: Bunkoczi, G. / Schiell, M. / Vertesy, L. / Sheldrick, G.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ob6.cif.gz | 24.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ob6.ent.gz | 20.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ob6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ob6_validation.pdf.gz | 420 KB | Display | wwPDB validaton report |
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Full document | 1ob6_full_validation.pdf.gz | 420.4 KB | Display | |
Data in XML | 1ob6_validation.xml.gz | 4.3 KB | Display | |
Data in CIF | 1ob6_validation.cif.gz | 5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ob/1ob6 ftp://data.pdbj.org/pub/pdb/validation_reports/ob/1ob6 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.99446, 0.01694, 0.10371), Vector: |
-Components
#1: Protein/peptide | Type: Peptaibol / Class: Antibiotic / Mass: 1669.017 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: CEPHAIBOL A IS A HEXADECAMERIC HELICAL PEPTIDE. THE N-TERM IS ACETYLATED (RESIDUE 0) Source: (natural) ACREMONIUM TUBAKII (fungus) / References: NOR: NOR00971, Cephaibol B #2: Chemical | #3: Chemical | ChemComp-ACT / | #4: Water | ChemComp-HOH / | Compound details | CEPHAIBOL B IS LINEAR PEPTIDE, A MEMBER OF THE PEPTAIBOL FAMILY OF MEMBRANE CHANNEL FORMING ...CEPHAIBOL B IS LINEAR PEPTIDE, A MEMBER OF THE PEPTAIBOL FAMILY OF MEMBRANE CHANNEL FORMING PEPTIDES. HERE, CEPHAIBOL B IS REPRESENTE | |
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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: 1.54 Å3/Da / Density % sol: 20 % | ||||||||||||||||||||||||
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Crystal grow | pH: 4.6 / Details: 0.1 M NAAC/HAC PH=4.6, 32% ETOH, pH 4.60 | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / PH range low: 4.8 / PH range high: 4.2 | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER M06XCE / Wavelength: 1.5418 |
Detector | Type: BRUKER SMART 6000 / Detector: CCD / Date: May 15, 2002 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 0.89→35.4 Å / Num. obs: 16045 / % possible obs: 97 % / Redundancy: 4.44 % / Rmerge(I) obs: 0.0437 / Net I/σ(I): 23.29 |
Reflection shell | Resolution: 0.89→1 Å / Redundancy: 2.16 % / Rmerge(I) obs: 0.0786 / Mean I/σ(I) obs: 10.37 / % possible all: 90 |
Reflection | *PLUS Highest resolution: 0.89 Å / Redundancy: 4.44 % / Num. measured all: 73436 / Rmerge(I) obs: 0.0437 |
Reflection shell | *PLUS % possible obs: 90 % / Rmerge(I) obs: 0.0786 / Mean I/σ(I) obs: 10.37 |
-Processing
Software |
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Refinement | Method to determine structure: DIRECT METHODS / Resolution: 0.89→35.4 Å / Num. parameters: 3121 / Num. restraintsaints: 4640 / Cross valid method: FREE R-VALUE / σ(F): 0 StereochEM target val spec case: RESTRAINTS FOR AIB, DIV, HYP AND PHL FROM ANTIAMOEBIN (PDB 1JOH) Stereochemistry target values: ENGH AND HUBER
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Solvent computation | Solvent model: MOEWS & KRETSINGER | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 10 / Occupancy sum hydrogen: 252 / Occupancy sum non hydrogen: 267.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.89→35.4 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 35.37 Å / Rfactor Rwork: 0.0746 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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