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Yorodumi- PDB-6ebx: STRUCTURE DETERMINATION OF A DIMERIC FORM OF ERABUTOXIN B, CRYSTA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ebx | ||||||
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Title | STRUCTURE DETERMINATION OF A DIMERIC FORM OF ERABUTOXIN B, CRYSTALLIZED FROM THIOCYANATE SOLUTION | ||||||
Components | ERABUTOXIN B | ||||||
Keywords | TOXIN | ||||||
Function / homology | Function and homology information acetylcholine receptor inhibitor activity / ion channel regulator activity / toxin activity / extracellular region Similarity search - Function | ||||||
Biological species | Laticauda semifasciata (broad-banded blue sea krait) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.7 Å | ||||||
Authors | Prange, T. / Saludjian, P. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.B / Year: 1992 Title: Structure determination of a dimeric form of erabutoxin-b, crystallized from a thiocyanate solution. Authors: Saludjian, P. / Prange, T. / Navaza, J. / Menez, R. / Guilloteau, J.P. / Ries-Kautt, M. / Ducruix, A. #1: Journal: To be Published Title: Crystallization of Basic Proteins by Ion Pairing Authors: Ries-Kautt, M. / Ducruix, A. #2: Journal: J.Biol.Chem. / Year: 1988 Title: Relative Effectiveness of Various Ions on the Solubility and Crystal Growth of Lysozyme Authors: Ries-Kautt, M. / Ducruix, A. #3: Journal: Acta Crystallogr.,Sect.A / Year: 1988 Title: Refinement at 1.4 Angstrom Resolution of a Model of Erabutoxin B: Treatment of Ordered Solvent and Discrete Disorder Authors: Smith, J.L. / Hendrickson, P.W.R.Corfield.W.A. / Low, B.W. #4: Journal: Eur.J.Biochem. / Year: 1985 Title: Erabutoxin B. Initial Protein Refinement and Sequence Analysis at 0.140-Nm Resolution Authors: Bourne, P.E. / Sato, A. / Corfield, P.W.R. / Rosen, L.S. / Birken, S. / Low, B.W. #5: Journal: Handb.Exp.Pharmacol. / Year: 1979 Title: The Three-Dimensional Structure of Postsynaptic Snake Neurotoxins. Consideration of Structure and Function Authors: Low, B.W. | ||||||
History |
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Remark 700 | SHEET THE TWO MOLECULES ARE ASSOCIATED VIA 1) AN INTERMOLECULAR ANTI-PARALLEL BETA SHEET ...SHEET THE TWO MOLECULES ARE ASSOCIATED VIA 1) AN INTERMOLECULAR ANTI-PARALLEL BETA SHEET ASSOCIATION AROUND THE TWO-FOLD NON-CRYSTALLOGRAPHIC AXIS AND 2) VIA INTERLEAVING OF FINGERS TWO AND THREE WITH MUTUAL TRP-29/PHE-32 STACKING. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ebx.cif.gz | 34.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ebx.ent.gz | 27.2 KB | Display | PDB format |
PDBx/mmJSON format | 6ebx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eb/6ebx ftp://data.pdbj.org/pub/pdb/validation_reports/eb/6ebx | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 6877.759 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Laticauda semifasciata (broad-banded blue sea krait) References: UniProt: Q90VW1 #2: Chemical | ChemComp-SCN / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.29 % | |||||||||||||||||||||||||
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Crystal grow | Details: CRYSTALLIZATION TOOK PLACE FROM KSCN SOLUTION (O.3M) AT PH 5.5 BY THE HANGING DROP METHOD AT ROOM TEMPERATURE. CRYSTALS APPEARED IN TWO WEEKS AS ELONGATED RODS. | |||||||||||||||||||||||||
Crystal grow | *PLUS pH: 4.5 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 1.7 Å / Num. obs: 11227 / % possible obs: 82 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.049 |
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Reflection shell | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 1.82 Å / Num. possible: 64 / Num. unique obs: 1577 |
-Processing
Software |
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Refinement | Highest resolution: 1.7 Å Details: SHIFTS FROM ENTRY *2EBX* IN POSITIONS OF NON-DISORDERED PROTEIN ATOMS ARE SMALL. THE RMS DEVIATION IS 0.5 ANGSTROMS FOR MAIN CHAIN ATOMS AND 0.9 FOR THE SIDE CHAIN ATOMS.
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Refinement step | Cycle: LAST / Highest resolution: 1.7 Å
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Software | *PLUS Name: 'X-PLOR, PROLSQ' / Classification: refinement | ||||||||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.194 | ||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||
Refine LS restraints | *PLUS
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