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- PDB-1w75: Native Orthorhombic form of Torpedo californica acetylcholinester... -

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Basic information

Entry
Database: PDB / ID: 1w75
TitleNative Orthorhombic form of Torpedo californica acetylcholinesterase (AChE)
ComponentsACETYLCHOLINESTERASE
KeywordsHYDROLASE / ALZHEIMER'S DISEASE / CHOLINESTERASE / GLYCOPROTEIN / GPI- ANCHOR / MUSCLE / NERVE / NEUROTRANSMITTER DEGRADATION / SERINE ESTERASE / SERINE HYDROLASE / SYNAPSE
Function / homology
Function and homology information


acetylcholine catabolic process in synaptic cleft / acetylcholinesterase / acetylcholinesterase activity / synaptic cleft / side of membrane / synapse / 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 / Alpha/Beta hydrolase fold ...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
Acetylcholinesterase
Similarity search - Component
Biological speciesTORPEDO CALIFORNICA (Pacific electric ray)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.4 Å
AuthorsGreenblatt, H.M. / Botti, S. / Argaman, A. / Silman, I. / Sussman, J.L.
Citation
Journal: J.Am.Chem.Soc. / Year: 2004
Title: The complex of a bivalent derivative of galanthamine with torpedo acetylcholinesterase displays drastic deformation of the active-site gorge: implications for structure-based drug design.
Authors: Greenblatt, H.M. / Guillou, C. / Guenard, D. / Argaman, A. / Botti, S. / Badet, B. / Thal, C. / Silman, I. / Sussman, J.L.
#1: Journal: Bioorg.Med.Chem. / Year: 1998
Title: Potent Acetylcholinesterase Inhibitors: Design, Synthesis, and Structure-Activity Relationships of Bis-Interacting Ligands in the Galanthamine Series
Authors: Mary, A. / Renko, D.Z. / Guillou, C. / Thal, C.
History
DepositionAug 29, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2004Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 10, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: citation / pdbx_database_proc ...citation / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Jul 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_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
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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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)123,5356
Polymers122,6502
Non-polymers8854
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)91.502, 106.586, 150.343
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99992, -0.01143, -0.00485), (-0.01155, 0.99962, 0.02521), (0.00456, 0.02527, -0.99967)
Vector: 183.61348, -0.44452, 101.03433)

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Components

#1: Protein ACETYLCHOLINESTERASE / / ACHE


Mass: 61325.090 Da / Num. of mol.: 2 / Fragment: RESIDUES 22-564 / 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-Acetylglucosamine


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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHREE N-TERMINAL RESIDUES AND 8 C-TERMINAL RESIDUES NOT SEEN IN DENSITY, AND NOT INCLUDED IN ...THREE N-TERMINAL RESIDUES AND 8 C-TERMINAL RESIDUES NOT SEEN IN DENSITY, AND NOT INCLUDED IN COORDINATE FILE. RESIDUES 486-489 HAVE POOR DENSITY, AND ARE NOT MODELED.

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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: 3.1 Å3/Da / Density % sol: 59.4 %
Crystal growDetails: PROTEIN IN 100MM NACL, 0.01%NAN3, 1MM MES PH6.5, MIXED 1/1 WITH SOLUBILIZED LI5 (PW11O39RHCH2COOH), 3 MICROLITER OF THIS MIXTURE WAS MIXED WITH 3 MICROLITER OF 40% PEG200 IN 0.5M MES PH5.8, ...Details: PROTEIN IN 100MM NACL, 0.01%NAN3, 1MM MES PH6.5, MIXED 1/1 WITH SOLUBILIZED LI5 (PW11O39RHCH2COOH), 3 MICROLITER OF THIS MIXTURE WAS MIXED WITH 3 MICROLITER OF 40% PEG200 IN 0.5M MES PH5.8, SUSPENDED OVER WELL WITH 36%PEG200 IN 0.5M MES, PH 5.8

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Aug 1, 2003 / Details: OSMIC BLUE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. obs: 55093 / % possible obs: 94.3 % / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Biso Wilson estimate: 42 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 4 / % possible all: 88.3

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 2.4→40 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.922 / SU B: 7.803 / SU ML: 0.18 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.357 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE TWO MOLECULES IN THE ASYMMETRIC UNIT ARE RELATED BY A NON-CRYSTALLOGRAPHIC TWO FOLD AXIS. NCS WAS NOT USED IN REFINEMENT. THE RESIDUES ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE TWO MOLECULES IN THE ASYMMETRIC UNIT ARE RELATED BY A NON-CRYSTALLOGRAPHIC TWO FOLD AXIS. NCS WAS NOT USED IN REFINEMENT. THE RESIDUES BETWEEN 485-490 ARE MISSING IN CHAIN A AND FIT IN CHAIN B.
RfactorNum. reflection% reflectionSelection details
Rfree0.247 2715 4.96 %RANDOM
Rwork0.204 ---
obs0.206 52293 94.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 32.87 Å2
Baniso -1Baniso -2Baniso -3
1--2.419 Å20 Å20 Å2
2--6.404 Å20 Å2
3----3.985 Å2
Refinement stepCycle: LAST / Resolution: 2.4→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8369 0 56 252 8677
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0218679
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5621.94411796
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.67551057
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1180.21252
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026684
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2210.24036
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.25953
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2427
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.214
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2760.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6941.55273
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.3428513
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.13533406
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3854.53283
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.307 181
Rwork0.26 3583
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0994-0.0220.01980.0436-0.04950.22010.0030.00010.0014-0.00540.00410.010.01590.0003-0.00720.04850.0002-0.00390.01040.02230.048585.60151.51721.163
20.15150.00150.02450.02490.0330.155-0.0095-0.00930.01440.00190.0156-0.00040.00350.0073-0.0060.04920.0033-0.00210.0158-0.01880.043997.33450.60281.552
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 535
2X-RAY DIFFRACTION2B4 - 535

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