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- PDB-5bwc: ACETYLCHOLINESTERASE (E.C. 3.1.1.7) FROM TORPEDO CALIFORNICA IN C... -

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Basic information

Entry
Database: PDB / ID: 5bwc
TitleACETYLCHOLINESTERASE (E.C. 3.1.1.7) FROM TORPEDO CALIFORNICA IN COMPLEX WITH THE BIS-PYRIDINIUM OXIME ORTHO-7
ComponentsAcetylcholinesterase
KeywordsHydrolase/Hydrolase inhibitor / Acetylcholinesterase / Hydrolase-Hydrolase inhibitor complex
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
1,7-HEPTYLENE-BIS-N,N'-SYN-2-PYRIDINIUMALDOXIME / Acetylcholinesterase
Similarity search - Component
Biological speciesTorpedo californica (Pacific electric ray)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsLegler, P.M. / Millard, C.B.
Funding support United States, 1items
OrganizationGrant numberCountry
Defense Threat Reduction Agency (DTRA)E0036_08_WR_C United States
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: A conformational change in the peripheral anionic site of Torpedo californica acetylcholinesterase induced by a bis-imidazolium oxime.
Authors: Legler, P.M. / Soojhawon, I. / Millard, C.B.
History
DepositionJun 7, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / 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_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5214
Polymers60,7371
Non-polymers7853
Water2,054114
1
A: Acetylcholinesterase
hetero molecules

A: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,0438
Polymers121,4732
Non-polymers1,5706
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_645y+1,x-1,-z1
Buried area2660 Å2
ΔGint-1 kcal/mol
Surface area41590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.152, 112.152, 137.328
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Acetylcholinesterase / AChE


Mass: 60736.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Torpedo californica (Pacific electric ray)
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.: 2
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
#3: Chemical ChemComp-HBP / 1,7-HEPTYLENE-BIS-N,N'-SYN-2-PYRIDINIUMALDOXIME


Mass: 342.435 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H26N4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 4.1 Å3/Da / Density % sol: 70.04 % / Description: Wedge shaped.
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: Drop solution contained 36% PEG 200, 0.2 M MES pH 5.8, 20 mM Ortho-7. Reservoir solution contained 35% PEG 200.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Jun 19, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.45→28.04 Å / Num. obs: 37229 / % possible obs: 99.9 % / Redundancy: 8.85 % / Rsym value: 0.1884 / Net I/σ(I): 9.31
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 7.83 % / Rmerge(I) obs: 0.4568 / Mean I/σ(I) obs: 4.05 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
SAINTdata reduction
SADABSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ACE

2ace


Resolution: 2.45→28.04 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.88 / Cross valid method: THROUGHOUT / ESU R: 0.305 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26641 1833 5 %RANDOM
Rwork0.24146 ---
obs0.24269 34919 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.766 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.45→28.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4244 0 53 114 4411
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0194424
X-RAY DIFFRACTIONr_bond_other_d00.024076
X-RAY DIFFRACTIONr_angle_refined_deg1.2891.9536003
X-RAY DIFFRACTIONr_angle_other_deg3.6239376
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1935531
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.33724.028211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.0515706
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5621524
X-RAY DIFFRACTIONr_chiral_restr0.0810.2628
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215025
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021081
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.832.0172127
X-RAY DIFFRACTIONr_mcbond_other0.8292.0152126
X-RAY DIFFRACTIONr_mcangle_it1.4683.0212657
X-RAY DIFFRACTIONr_mcangle_other1.4683.0232658
X-RAY DIFFRACTIONr_scbond_it0.8152.1522297
X-RAY DIFFRACTIONr_scbond_other0.8152.1522296
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.4493.1833347
X-RAY DIFFRACTIONr_long_range_B_refined2.77815.9745104
X-RAY DIFFRACTIONr_long_range_B_other2.75215.9875084
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.45→2.513 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 129 -
Rwork0.293 2551 -
obs--100 %

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