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Yorodumi- PDB-1kv0: Cis/trans Isomerization of Non-prolyl Peptide Bond Observed in Cr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kv0 | ||||||
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Title | Cis/trans Isomerization of Non-prolyl Peptide Bond Observed in Crystal Structure of an Scorpion Toxin | ||||||
Components | Alpha-like toxin BmK-M7 | ||||||
Keywords | TOXIN / Non-prolyl cis peptide bond / Cis/trans isomerization / Dimeric structure / Scorpion toxin | ||||||
Function / homology | Function and homology information sodium channel inhibitor activity / : / defense response / toxin activity / extracellular region Similarity search - Function | ||||||
Biological species | Mesobuthus martensii (Chinese scorpion) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Guan, R.J. / He, X.L. / Wang, M. / Xiang, Y. / Wang, D.C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: Structural mechanism governing cis and trans isomeric states and an intramolecular switch for cis/trans isomerization of a non-proline peptide bond observed in crystal structures of scorpion toxins. Authors: Guan, R.J. / Xiang, Y. / He, X.L. / Wang, C.G. / Wang, M. / Zhang, Y. / Sundberg, E.J. / Wang, D.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kv0.cif.gz | 67.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kv0.ent.gz | 51 KB | Display | PDB format |
PDBx/mmJSON format | 1kv0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kv0_validation.pdf.gz | 427.2 KB | Display | wwPDB validaton report |
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Full document | 1kv0_full_validation.pdf.gz | 429.5 KB | Display | |
Data in XML | 1kv0_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 1kv0_validation.cif.gz | 11.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kv/1kv0 ftp://data.pdbj.org/pub/pdb/validation_reports/kv/1kv0 | HTTPS FTP |
-Related structure data
Related structure data | 1t7aC 1t7bC 1t7eC 1sn1S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 7252.350 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mesobuthus martensii (Chinese scorpion) / Tissue: tail venom gland / References: UniProt: P59854 #2: Water | ChemComp-HOH / | |
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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: 1.89 Å3/Da / Density % sol: 34.81 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: ammonium sulfate, Tris-HCl, Ethanol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 24, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→29.3 Å / Num. obs: 19260 / % possible obs: 85.8 % / Observed criterion σ(F): 0 / Rmerge(I) obs: 0.04 |
Reflection shell | Resolution: 1.4→1.48 Å / Rmerge(I) obs: 0.201 / Mean I/σ(I) obs: 3.6 / % possible all: 74.6 |
Reflection | *PLUS Highest resolution: 1.4 Å / Num. measured all: 57131 / Rmerge(I) obs: 0.04 |
Reflection shell | *PLUS % possible obs: 74.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1SN1 Resolution: 1.4→29.49 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.964 / SU B: 0.795 / SU ML: 0.032 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.774 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→29.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20
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Refinement | *PLUS Lowest resolution: 29.3 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.164 / Rfactor Rwork: 0.142 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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