+Open data
-Basic information
Entry | Database: PDB / ID: 1qkd | ||||||
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Title | ERABUTOXIN | ||||||
Components | ERABUTOXIN A | ||||||
Keywords | NEUROTOXIN / ERABUTOXIN | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å | ||||||
Authors | Nastopoulos, V. / Kanellopoulos, P.N. / Tsernoglou, D. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1998 Title: Structure of dimeric and monomeric erabutoxin a refined at 1.5 A resolution. Authors: Nastopoulos, V. / Kanellopoulos, P.N. / Tsernoglou, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qkd.cif.gz | 36.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qkd.ent.gz | 28.4 KB | Display | PDB format |
PDBx/mmJSON format | 1qkd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qkd_validation.pdf.gz | 419.2 KB | Display | wwPDB validaton report |
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Full document | 1qkd_full_validation.pdf.gz | 421.5 KB | Display | |
Data in XML | 1qkd_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | 1qkd_validation.cif.gz | 14.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qk/1qkd ftp://data.pdbj.org/pub/pdb/validation_reports/qk/1qkd | HTTPS FTP |
-Related structure data
Related structure data | 1qkeC 6ebxS 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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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.998, -0.0264, -0.0579), Vector: |
-Components
#1: Protein | Mass: 6853.715 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: JAPANESE SEA SNAKE Source: (natural) Laticauda semifasciata (broad-banded blue sea krait) Secretion: VENOM / References: UniProt: P60775 #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: 2.2 Å3/Da / Density % sol: 44.1 % | |||||||||||||||
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Crystal grow | pH: 7.2 / Details: pH 7.2 | |||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.92 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1992 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→17.4 Å / Num. obs: 19420 / % possible obs: 94.8 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 25.8 Å2 / Rsym value: 0.065 / Net I/σ(I): 29.7 |
Reflection shell | Resolution: 1.49→1.6 Å / Redundancy: 14 % / Mean I/σ(I) obs: 5.25 / Rsym value: 0.204 / % possible all: 86 |
Reflection | *PLUS Rmerge(I) obs: 0.065 |
Reflection shell | *PLUS % possible obs: 86 % / Rmerge(I) obs: 0.204 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6EBX Resolution: 1.49→17.4 Å / σ(F): 0 / Details: X-PLOR WAS ALSO USED
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Refinement step | Cycle: LAST / Resolution: 1.49→17.4 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5EA / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 25.8 Å2 | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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