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- PDB-7b2w: Torpedo californica acetylcholinesterase complexed with UO2 -

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Basic information

Entry
Database: PDB / ID: 7b2w
TitleTorpedo californica acetylcholinesterase complexed with UO2
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / acetylcholinesterase / ASSAM / differential scanning calorimetry / divalent metal ion / electron paramagnetic resonance / thermal inactivation / Torpedo / 4D motif / 3.1.1.7
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
Similarity search - Domain/homology
URANYL (VI) ION / Acetylcholinesterase
Similarity search - Component
Biological speciesTetronarce californica (Pacific electric ray)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsSilman, I. / Shnyrov, V.L. / Ashani, Y. / Roth, E. / Nicolas, A. / Sussman, J.L. / Weiner, L.
Citation
Journal: Protein Sci. / Year: 2021
Title: Torpedo californica acetylcholinesterase is stabilized by binding of a divalent metal ion to a novel and versatile 4D motif.
Authors: Silman, I. / Shnyrov, V.L. / Ashani, Y. / Roth, E. / Nicolas, A. / Sussman, J.L. / Weiner, L.
#1: Journal: Bull Soc Ophtalmol Fr / Year: 1987
Title: [Treatment of vitreous hemorrhages. Rare causes].
Authors: Aracil, P.
#2: Journal: Science / Year: 1991
Title: Atomic structure of acetylcholinesterase from Torpedo californica: a prototypic acetylcholine-binding protein.
Authors: Sussman, J.L. / Harel, M. / Frolow, F. / Oefner, C. / Goldman, A. / Toker, L. / Silman, I.
History
DepositionNov 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Apr 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: 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 1.4Nov 6, 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

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Assembly

Deposited unit
A: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2773
Polymers60,7371
Non-polymers5402
Water48627
1
A: Acetylcholinesterase
hetero molecules

A: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,5536
Polymers121,4732
Non-polymers1,0804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area2800 Å2
ΔGint-21 kcal/mol
Surface area35950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.880, 110.880, 134.670
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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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) Tetronarce californica (Pacific electric ray)
Organ: ELECTRIC ORGAN / Variant: G2 FORM / Tissue: ELECTROPLAQUE / References: UniProt: P04058, acetylcholinesterase
#2: Chemical ChemComp-IUM / URANYL (VI) ION


Mass: 270.028 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2U / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.93 Å3/Da / Density % sol: 68.74 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: The use of standard vapor diffusion techniques in hanging drop with 61 percent saturated ammonium sulfate, 360 nM Na,K-phosphate buffer pH 7.0, as the precipating agent and a protein ...Details: The use of standard vapor diffusion techniques in hanging drop with 61 percent saturated ammonium sulfate, 360 nM Na,K-phosphate buffer pH 7.0, as the precipating agent and a protein concentration of ~11 mg/ml together with UO2(NO3)2.

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.541 Å
DetectorType: SIEMENS-XENTRONICS / Detector: AREA DETECTOR / Date: Jul 10, 1990
RadiationMonochromator: Graphite monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 2.65→39.0924 Å / Num. obs: 23867 / % possible obs: 84.24 % / Biso Wilson estimate: 36.6 Å2 / Rsym value: 0.115 / Net I/σ(I): 13.6
Reflection shellResolution: 2.65→2.77 Å / Mean I/σ(I) obs: 1.44 / Num. unique obs: 2116 / Rsym value: 0.09 / % possible all: 57.9

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Processing

Software
NameVersionClassification
PHENIX1.19rc7_4070-000refinement
REFMAC5.8.0267refinement
DENZOV1.0data reduction
SCALEPACKV1.0data scaling
MERLOTV1.0phasing
Coot9.3model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EA5

1ea5


Resolution: 2.65→39.09 Å / SU ML: 0.3211 / Cross valid method: FREE R-VALUE / σ(F): 1.57 / Phase error: 20.046
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2124 2001 8.39 %
Rwork0.1613 21863 -
obs0.1656 23864 84.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.31 Å2
Refinement stepCycle: LAST / Resolution: 2.65→39.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4187 0 6 27 4220
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01244322
X-RAY DIFFRACTIONf_angle_d1.32255870
X-RAY DIFFRACTIONf_chiral_restr0.0642619
X-RAY DIFFRACTIONf_plane_restr0.0107763
X-RAY DIFFRACTIONf_dihedral_angle_d7.128574
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.720.3533810.2573908X-RAY DIFFRACTION49.82
2.72-2.790.26951070.23791186X-RAY DIFFRACTION64.78
2.79-2.870.34811170.23761287X-RAY DIFFRACTION70.52
2.87-2.960.29611280.22961387X-RAY DIFFRACTION75.79
2.96-3.070.27071290.20971464X-RAY DIFFRACTION80.01
3.07-3.190.29861380.21391504X-RAY DIFFRACTION81.85
3.19-3.340.25181470.17981564X-RAY DIFFRACTION85.64
3.34-3.510.22631510.15591637X-RAY DIFFRACTION88.82
3.51-3.730.18051510.14121699X-RAY DIFFRACTION91.63
3.73-4.020.18091600.12931719X-RAY DIFFRACTION93.39
4.02-4.430.15391610.12031826X-RAY DIFFRACTION96.74
4.43-5.070.1811690.11711832X-RAY DIFFRACTION98.77
5.07-6.380.19211750.15771882X-RAY DIFFRACTION99.66
6.38-39.090.18891870.16781968X-RAY DIFFRACTION99.63

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