+Open data
-Basic information
Entry | Database: PDB / ID: 1i9b | ||||||
---|---|---|---|---|---|---|---|
Title | X-RAY STRUCTURE OF ACETYLCHOLINE BINDING PROTEIN (ACHBP) | ||||||
Components | ACETYLCHOLINE BINDING PROTEIN | ||||||
Keywords | LIGAND BINDING PROTEIN / pentamer / igg fold | ||||||
Function / homology | Function and homology information extracellular ligand-gated monoatomic ion channel activity / synaptic cleft / transmembrane signaling receptor activity / synapse / membrane Similarity search - Function | ||||||
Biological species | Lymnaea stagnalis (great pond snail) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å | ||||||
Authors | Brejc, K. / van Dijk, W.J. / Klaassen, R. / Schuurmans, M. / van der Oost, J. / Smit, A.B. / Sixma, T.K. | ||||||
Citation | Journal: Nature / Year: 2001 Title: Crystal structure of an ACh-binding protein reveals the ligand-binding domain of nicotinic receptors. Authors: Brejc, K. / van Dijk, W.J. / Klaassen, R.V. / Schuurmans, M. / van Der Oost, J. / Smit, A.B. / Sixma, T.K. #1: Journal: Nature / Year: 2001 Title: A glia-derived acetylcholine-binding protein that modulates synaptic transmission Authors: Smit, A.B. / Syed, N.I. / Schaap, D. / van Minnen, J. / Klumperman, J. / Kits, K.S. / Lodder, H. / van der Schors, R.C. / van Elk, R. / Sorgedrager, B. / Brejc, K. / Sixma, T.K. / Geraerts, W.P.M. | ||||||
History |
| ||||||
Remark 999 | SEQUENCE THE SEQUENCE FOR THE PROTEIN IS NOT YET DEPOSITED IN THE SEQUENCE DATABASE. THE EXPRESSED ...SEQUENCE THE SEQUENCE FOR THE PROTEIN IS NOT YET DEPOSITED IN THE SEQUENCE DATABASE. THE EXPRESSED PROTEIN HAS A MUATAION AT RESIDUE 1: L1F. RESIDUES -6 TO 0 (EAEAYVE) ARE CLONING ARTIFACTS. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1i9b.cif.gz | 206.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1i9b.ent.gz | 176.7 KB | Display | PDB format |
PDBx/mmJSON format | 1i9b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i9/1i9b ftp://data.pdbj.org/pub/pdb/validation_reports/i9/1i9b | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 24688.342 Da / Num. of mol.: 5 / Mutation: L1F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lymnaea stagnalis (great pond snail) / Plasmid: PPIC9 / Production host: Pichia pastoris (fungus) / Strain (production host): GS 115 / References: UniProt: P58154 #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-EPE / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 48 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 4000, CALCIUM CHLORIDE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X11 / Wavelength: 0.943 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.943 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→44 Å / Num. all: 34483 / Num. obs: 34483 / % possible obs: 97.8 % / Observed criterion σ(I): 2.3 / Redundancy: 6.5 % / Biso Wilson estimate: 57.3 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 27.4 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.674 / Mean I/σ(I) obs: 2.3 / % possible all: 96.5 |
Reflection | *PLUS |
Reflection shell | *PLUS % possible obs: 96.5 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 2.7→19.97 Å / Rfactor Rfree error: 0.008 / Data cutoff high rms absF: 2515375.59 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 28.86 Å2 / ksol: 0.321 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.4 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→19.97 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.7 Å / σ(F): 0 / % reflection Rfree: 4.6 % / Rfactor obs: 0.26 / Rfactor Rwork: 0.26 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 61.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.434 / % reflection Rfree: 4.5 % / Rfactor Rwork: 0.4 |