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- PDB-2vjb: Torpedo Californica Acetylcholinesterase In Complex With A Non Hy... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2vjb | ||||||
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Title | Torpedo Californica Acetylcholinesterase In Complex With A Non Hydrolysable Substrate Analogue, 4-Oxo-N,N,N- Trimethylpentanaminium - Orthorhombic space group - Dataset D at 100K | ||||||
![]() | ACETYLCHOLINESTERASE | ||||||
![]() | HYDROLASE / SERINE ESTERASE / ALTERNATIVE SPLICING / NEUROTRANSMITTER DEGRADATION / KINETIC CRYSTALLOGRAPHY / STRUCTURAL DYNAMICS / XRAY DAMAGE / SUBSTRATE ANALOGUE / LIPOPROTEIN / GLYCOPROTEIN / CELL JUNCTION / SYNAPSE / MEMBRANE / GPI-ANCHOR | ||||||
Function / homology | ![]() acetylcholine catabolic process in synaptic cleft / acetylcholinesterase / acetylcholinesterase activity / choline metabolic process / side of membrane / synaptic cleft / synapse / extracellular space / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Colletier, J.P. / Bourgeois, D. / Fournier, D. / Silman, I. / Sussman, J.L. / Weik, M. | ||||||
![]() | ![]() Title: Shoot-and-Trap: Use of Specific X-Ray Damage to Study Structural Protein Dynamics by Temperature-Controlled Cryo-Crystallography. Authors: Colletier, J.P. / Bourgeois, D. / Sanson, B. / Fournier, D. / Sussman, J.L. / Silman, I. / Weik, M. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 260.9 KB | Display | ![]() |
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PDB format | ![]() | 209.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 496.1 KB | Display | ![]() |
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Full document | ![]() | 533.6 KB | Display | |
Data in XML | ![]() | 64.1 KB | Display | |
Data in CIF | ![]() | 96.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2vjaC ![]() 2vjcC ![]() 2vjdC ![]() 2vt6C ![]() 2vt7C ![]() 1w75S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
-Protein / Sugars , 2 types, 6 molecules AB![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#1: Protein | Mass: 60736.516 Da / Num. of mol.: 2 / Fragment: RESIDUES 22-558 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Organ: ELECTRIC ORGAN / Variant: G2 FORM / Tissue: ELECTROPLAQUE / References: UniProt: P04058, acetylcholinesterase #2: Sugar | ChemComp-NAG / |
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-Non-polymers , 4 types, 1612 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/CCD.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CCD.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-CCD / ( #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | 4-OXO-N,N,N- TRIMETHYLPENTANAMINIUM (CCD): ALREADY PRESENT IN PDB ENTRY 2C5F - IT IS COVALENTLY ...4-OXO-N,N,N- TRIMETHYLP |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 56 % / Description: NONE |
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Crystal grow | Temperature: 277 K / pH: 6 Details: 32% PEG200, 150MM MES, PH6, 4 DEG. C. 2 HOURS SOAKING IN MOTHER LIQUOR SOLUTION CONTAINING 0.5 MM OTMA, pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 21, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93224 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 59627 / % possible obs: 99.4 % / Observed criterion σ(I): 3.5 / Redundancy: 7.2 % / Biso Wilson estimate: 26.9 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 2.4→2.5 Å / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 4 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1W75 Resolution: 2.39→46.35 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3716067.5 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 57.1714 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.39→46.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
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Xplor file |
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