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- PDB-2v97: Structure of the unphotolysed complex of TcAChE with 1-(2- nitrop... -

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Basic information

Entry
Database: PDB / ID: 2v97
TitleStructure of the unphotolysed complex of TcAChE with 1-(2- nitrophenyl)-2,2,2-trifluoroethyl-arsenocholine after a 9 seconds annealing to room temperature
ComponentsACETYLCHOLINESTERASE
KeywordsHYDROLASE / PARTIAL Q-WEIGHTED DIFFERENCE REFINEMENT / NEUROTRANSMITTER DEGRADATION / ALTERNATIVE SPLICING / KINETIC CRYSTALLOGRAPHY / SERINE ESTERASE / CAGED COMPOUNDS / ACETYLCHOLINESTERASE / SYNAPSE / MEMBRANE / BACKDOOR / GPI-ANCHOR / LIPOPROTEIN / GLYCOPROTEIN / CELL JUNCTION
Function / homology
Function and homology information


acetylcholine catabolic process in synaptic cleft / choline metabolic process / acetylcholinesterase / acetylcholinesterase activity / synaptic cleft / side of membrane / synapse / extracellular space / plasma membrane
Similarity search - Function
Acetylcholinesterase, fish/snake / : / Cholinesterase / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold, catalytic domain ...Acetylcholinesterase, fish/snake / : / Cholinesterase / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-CFQ / Acetylcholinesterase
Similarity search - Component
Biological speciesTORPEDO CALIFORNICA (Pacific electric ray)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsColletier, J.-P. / Sanson, B. / Royant, A. / Specht, A. / Nachon, F. / Masson, P. / Zaccai, G. / Sussman, J.L. / Goeldner, M. / Silman, I. ...Colletier, J.-P. / Sanson, B. / Royant, A. / Specht, A. / Nachon, F. / Masson, P. / Zaccai, G. / Sussman, J.L. / Goeldner, M. / Silman, I. / Bourgeois, D. / Weik, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Use of a 'Caged' Analog to Study Traffic of Choline within Acetylcholinesterase by Kinetic Crystallography
Authors: Colletier, J.-P. / Royant, A. / Specht, A. / Sanson, B. / Nachon, F. / Masson, P. / Zaccai, G. / Sussman, J.L. / Goeldner, M. / Silman, I. / Bourgeois, D. / Weik, M.
History
DepositionAug 22, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5May 12, 2021Group: Derived calculations / Structure summary
Category: chem_comp / pdbx_struct_assembly ...chem_comp / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _chem_comp.pdbx_synonyms
Revision 1.6Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.7Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ACETYLCHOLINESTERASE
B: ACETYLCHOLINESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,87011
Polymers121,4732
Non-polymers2,3979
Water35,0031943
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint18 kcal/mol
Surface area37700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.200, 104.460, 148.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ACETYLCHOLINESTERASE / ACHE


Mass: 60736.516 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) TORPEDO CALIFORNICA (Pacific electric ray)
Organ: ELECTRIC ORGAN / Variant: G2 FORM / Tissue: ELECTROPLAQUE / References: UniProt: P04058, acetylcholinesterase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-CFQ / 1-(2-nitrophenyl)-2,2,2-trifluoroethyl]-arsenocholine


Mass: 369.212 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H19AsF3NO3
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1943 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal growTemperature: 277 K / pH: 6
Details: 32% PEG200, 150MM MES, PH6, 4 DEG. C. THE CRYSTAL WAS SOAKED IN A MOTHER LIQUOR SOLUTION CONTAINING 0.5MM CAGED ARSENOCHOLINE DURING 12 HOURS, IN THE DARK AND AT 4 DEG. C., pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93224
DetectorType: ADSC CCD / Detector: CCD / Date: May 20, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93224 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 106579 / % possible obs: 99.8 % / Observed criterion σ(I): 2.5 / Redundancy: 3.8 % / Biso Wilson estimate: 25.6 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.42
Reflection shellResolution: 2.4→2.55 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.83 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
XDSdata reduction
XSCALEdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W75

1w75


Resolution: 2.4→19.81 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3637820.18 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.272 5316 5 %RANDOM
Rwork0.207 ---
obs0.207 106580 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.0628 Å2 / ksol: 0.289 e/Å3
Displacement parametersBiso mean: 38.3 Å2
Baniso -1Baniso -2Baniso -3
1--15.39 Å20 Å20 Å2
2--20.54 Å20 Å2
3----5.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8380 0 141 1943 10464
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.4→2.44 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.436 263 5 %
Rwork0.382 5049 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION4CFN.PARAMCFN.TOP
X-RAY DIFFRACTION5ION.PARAMION.TOP

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