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Yorodumi- PDB-6m4z: Co-crystal structure of Ac-AChBPP in complex with alpha-conotoxin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6m4z | ||||||
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Title | Co-crystal structure of Ac-AChBPP in complex with alpha-conotoxin [D11A]LvIA | ||||||
Components |
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Keywords | METAL BINDING PROTEIN/TOXIN / conotoxin / AChBP / METAL BINDING PROTEIN-TOXIN complex | ||||||
Function / homology | Function and homology information host cell postsynaptic membrane / acetylcholine receptor inhibitor activity / ion channel regulator activity / excitatory extracellular ligand-gated monoatomic ion channel activity / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / transmembrane signaling receptor activity / toxin activity / postsynapse / neuron projection / extracellular region ...host cell postsynaptic membrane / acetylcholine receptor inhibitor activity / ion channel regulator activity / excitatory extracellular ligand-gated monoatomic ion channel activity / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / transmembrane signaling receptor activity / toxin activity / postsynapse / neuron projection / extracellular region / identical protein binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Aplysia californica (California sea hare) Conus lividus (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.803 Å | ||||||
Authors | Wang, X.Q. / Pan, S. / Luo, S.L. / Zhu, X.P. | ||||||
Citation | Journal: To Be Published Title: The crystal structure of Ac-AChBP in complex with LvIA analogs reveals the mechanism of its selectivity towards different nAChR subtypes Authors: Zhu, X.P. / Pan, S. / Wang, X.Q. / Luo, S.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6m4z.cif.gz | 226.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6m4z.ent.gz | 184 KB | Display | PDB format |
PDBx/mmJSON format | 6m4z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6m4z_validation.pdf.gz | 495.4 KB | Display | wwPDB validaton report |
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Full document | 6m4z_full_validation.pdf.gz | 528.2 KB | Display | |
Data in XML | 6m4z_validation.xml.gz | 42.7 KB | Display | |
Data in CIF | 6m4z_validation.cif.gz | 58.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m4/6m4z ftp://data.pdbj.org/pub/pdb/validation_reports/m4/6m4z | HTTPS FTP |
-Related structure data
Related structure data | 6m4xC 5co5S 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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-Components
#1: Protein | Mass: 23535.307 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aplysia californica (California sea hare) Production host: Baculovirus expression vector pCTdual / References: UniProt: Q8WSF8 #2: Protein/peptide | Mass: 1640.908 Da / Num. of mol.: 5 / Mutation: D31A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Conus lividus (invertebrata) / Production host: Synthesium tursionis (invertebrata) / References: UniProt: L8BU87 Has ligand of interest | Y | Has protein modification | Y | |
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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: 4.08 Å3/Da / Density % sol: 69.83 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 1.2 M Sodium citrate tribasic dihydrate, 0.1 M BIS-TRIS propane (pH 7.0) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.62 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Sep 19, 2017 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.62 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.68→50 Å / Num. obs: 55659 / % possible obs: 98.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 84.57 Å2 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.048 / Rrim(I) all: 0.095 / Χ2: 1.021 / Net I/σ(I): 7.8 / Num. measured all: 207813 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5CO5 Resolution: 2.803→39.223 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.9 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 147.48 Å2 / Biso mean: 83.0101 Å2 / Biso min: 30 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.803→39.223 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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