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- PDB-2vjd: Torpedo Californica Acetylcholinesterase In Complex With A Non Hy... -

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Basic information

Entry
Database: PDB / ID: 2vjd
TitleTorpedo Californica Acetylcholinesterase In Complex With A Non Hydrolysable Substrate Analogue, 4-Oxo-N,N,N- Trimethylpentanaminium - Orthorhombic space group - Dataset C at 150K
ComponentsACETYLCHOLINESTERASE
KeywordsHYDROLASE / SERINE ESTERASE / ALTERNATIVE SPLICING / NEUROTRANSMITTER DEGRADATION / KINETIC CRYSTALLOGRAPHY / STRUCTURAL DYNAMICS / XRAY DAMAGE / SUBSTRATE ANALOGUE / LIPOPROTEIN / GLYCOPROTEIN / CELL JUNCTION / SYNAPSE / MEMBRANE / GPI-ANCHOR
Function / homology
Function and homology information


acetylcholine catabolic process in synaptic cleft / acetylcholinesterase / choline metabolic process / acetylcholinesterase activity / synaptic cleft / side of membrane / synapse / extracellular space / plasma membrane
Similarity search - Function
Acetylcholinesterase, fish/snake / : / Cholinesterase / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold, catalytic domain ...Acetylcholinesterase, fish/snake / : / Cholinesterase / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / 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
(4R)-4-HYDROXY-N,N,N-TRIMETHYLPENTAN-1-AMINIUM / TRIETHYLENE GLYCOL / Acetylcholinesterase
Similarity search - Component
Biological speciesTORPEDO CALIFORNICA (Pacific electric ray)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsColletier, J.P. / Bourgeois, D. / Fournier, D. / Silman, I. / Sussman, J.L. / Weik, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2008
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.
History
DepositionDec 9, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2008Provider: 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 / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / 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 / _struct_conn.pdbx_role
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 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACETYLCHOLINESTERASE
B: ACETYLCHOLINESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,53517
Polymers121,4732
Non-polymers2,06215
Water28,8421601
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint1 kcal/mol
Surface area39640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.980, 107.540, 151.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 6 molecules AB

#1: Protein ACETYLCHOLINESTERASE / ACHE


Mass: 60736.516 Da / Num. of mol.: 2 / Fragment: RESIDUES 22-558 / 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: 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

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Non-polymers , 4 types, 1612 molecules

#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-CCD / (4R)-4-HYDROXY-N,N,N-TRIMETHYLPENTAN-1-AMINIUM


Mass: 146.250 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H20NO
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1601 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer details4-OXO-N,N,N- TRIMETHYLPENTANAMINIUM (CCD): ALREADY PRESENT IN PDB ENTRY 2C5F - IT IS COVALENTLY ...4-OXO-N,N,N- TRIMETHYLPENTANAMINIUM (CCD): ALREADY PRESENT IN PDB ENTRY 2C5F - IT IS COVALENTLY BOUND TO CATALYTIC SERINE 200

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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: 2.62 Å3/Da / Density % sol: 52.77 % / Description: NONE
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93224
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 21, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93224 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 59320 / % possible obs: 99.9 % / Observed criterion σ(I): 3.5 / Redundancy: 7.2 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.1
Reflection shellResolution: 2.4→2.5 Å / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 4.6 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.2refinement
XDSdata reduction
XSCALEdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W75

1w75


Resolution: 2.3→45.99 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3501668.02 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.25 3366 5 %RANDOM
Rwork0.196 ---
obs0.196 67283 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.7597 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 40.1 Å2
Baniso -1Baniso -2Baniso -3
1--5.25 Å20 Å20 Å2
2--15.06 Å20 Å2
3----9.82 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.3→45.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8454 0 130 1601 10185
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.3
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_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it2.142
X-RAY DIFFRACTIONc_scbond_it2.082
X-RAY DIFFRACTIONc_scangle_it3.112.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.313 555 5 %
Rwork0.268 10527 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CARBOHYDRATE.PARAMION.TOP
X-RAY DIFFRACTION4ION.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION5AS.PARAMAS.TOP

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