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

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Basic information

Entry
Database: PDB / ID: 5bwb
TitleACETYLCHOLINESTERASE (E.C. 3.1.1.7) FROM TORPEDO CALIFORNICA IN COMPLEX WITH THE BIS-IMIDAZOLIUM OXIME 2BIM-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 / side of membrane / synaptic cleft / synapse / : / 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-4VV / Acetylcholinesterase
Similarity search - Component
Biological speciesTorpedo californica (Pacific electric ray)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.57 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 9, 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)61,6975
Polymers60,7371
Non-polymers9604
Water3,729207
1
A: Acetylcholinesterase
hetero molecules

A: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,39310
Polymers121,4732
Non-polymers1,9208
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area3270 Å2
ΔGint7 kcal/mol
Surface area39530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.303, 112.303, 137.114
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 / Fragment: UNP residues 22-558 / 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-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-4VV / (Z,Z)-[heptane-1,7-diylbis(1H-imidazol-1-yl-2-ylidene)]bis(N-hydroxymethanamine)


Mass: 322.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H26N6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 4.11 Å3/Da / Density % sol: 70.07 % / Description: wedge shaped
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: Drop solution contained 36% PEG 200, 0.2 M MES buffer pH 5.7, 20 mM 2BIM-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: Dec 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.57→56.15 Å / Num. obs: 32414 / % possible obs: 100 % / Redundancy: 13.58 % / Rsym value: 0.1245 / Net I/σ(I): 17.18
Reflection shellResolution: 2.57→2.66 Å / Redundancy: 13.6 % / Rmerge(I) obs: 0.4065 / Mean I/σ(I) obs: 5.59 / % 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: 2.57→56.15 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.901 / Cross valid method: THROUGHOUT / ESU R: 0.345 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24197 1580 5.1 %RANDOM
Rwork0.20863 ---
obs0.21032 29650 96.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.291 Å2
Baniso -1Baniso -2Baniso -3
1-1.11 Å20.56 Å2-0 Å2
2--1.11 Å20 Å2
3----3.6 Å2
Refinement stepCycle: 1 / Resolution: 2.57→56.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4245 0 63 207 4515
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194437
X-RAY DIFFRACTIONr_bond_other_d00.024081
X-RAY DIFFRACTIONr_angle_refined_deg2.1691.9576023
X-RAY DIFFRACTIONr_angle_other_deg3.69239393
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5655531
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.7624.028211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.415706
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0941524
X-RAY DIFFRACTIONr_chiral_restr0.1870.2630
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0215029
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021073
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_it0.753.2822127
X-RAY DIFFRACTIONr_mcbond_other0.7483.2812126
X-RAY DIFFRACTIONr_mcangle_it1.1884.9222657
X-RAY DIFFRACTIONr_mcangle_other1.1884.9232658
X-RAY DIFFRACTIONr_scbond_it0.8443.4162310
X-RAY DIFFRACTIONr_scbond_other0.8433.4162311
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3615.0853367
X-RAY DIFFRACTIONr_long_range_B_refined2.97126.1675079
X-RAY DIFFRACTIONr_long_range_B_other2.78426.1555023
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.57→2.637 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 133 -
Rwork0.251 2176 -
obs--97.51 %

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