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- PDB-4b0p: Crystal structure of soman-aged human butyrylcholinesterase in co... -

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Basic information

Entry
Database: PDB / ID: 4b0p
TitleCrystal structure of soman-aged human butyrylcholinesterase in complex with methyl 2-(pentafluorobenzyloxyimino)pyridinium
ComponentsCHOLINESTERASE
KeywordsHYDROLASE / AGING
Function / homology
Function and homology information


cholinesterase / : / neuroblast differentiation / response to folic acid / choline binding / Neurotransmitter clearance / cholinesterase activity / response to alkaloid / choline metabolic process / acetylcholine catabolic process ...cholinesterase / : / neuroblast differentiation / response to folic acid / choline binding / Neurotransmitter clearance / cholinesterase activity / response to alkaloid / choline metabolic process / acetylcholine catabolic process / negative regulation of synaptic transmission / peptide hormone processing / hydrolase activity, acting on ester bonds / acetylcholinesterase activity / Aspirin ADME / Synthesis of PC / nuclear envelope lumen / catalytic activity / Synthesis, secretion, and deacylation of Ghrelin / xenobiotic metabolic process / response to glucocorticoid / learning / amyloid-beta binding / blood microparticle / endoplasmic reticulum lumen / negative regulation of cell population proliferation / enzyme binding / extracellular space / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / : / 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 ...Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / : / 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
GLYCINE / : / Chem-MF5 / Cholinesterase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWandhammer, M. / de Koning, M. / van Grol, M. / Noort, D. / Goeldner, M. / Nachon, F.
CitationJournal: Chem.Biol.Interact / Year: 2013
Title: A Step Toward the Reactivation of Aged Cholinesterases -Crystal Structure of Ligands Binding to Aged Human Butyrylcholinesterase
Authors: Wandhammer, M. / De Koning, M. / Van Grol, M. / Loiodice, M. / Saurel, L. / Noort, D. / Goeldner, M. / Nachon, F.
History
DepositionJul 4, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2012Group: Database references
Revision 1.2Apr 17, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CHOLINESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,59720
Polymers59,7921
Non-polymers2,80519
Water3,387188
1
A: CHOLINESTERASE
hetero molecules

A: CHOLINESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,19440
Polymers119,5832
Non-polymers5,61138
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_555-y+1/2,-x+1/2,-z+1/21
Buried area9020 Å2
ΔGint-104.3 kcal/mol
Surface area41880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.230, 154.230, 133.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

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Protein , 1 types, 1 molecules A

#1: Protein CHOLINESTERASE / BUTYRYLCHOLINESTERASE / ACYLCHOLINE ACYLHYDROLASE / BUTYRYLCHOLINE ESTERASE / CHOLINE ESTERASE II / ...BUTYRYLCHOLINESTERASE / ACYLCHOLINE ACYLHYDROLASE / BUTYRYLCHOLINE ESTERASE / CHOLINE ESTERASE II / PSEUDOCHOLINESTERASE


Mass: 59791.512 Da / Num. of mol.: 1 / Fragment: RESIDUES 29-557
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGS / Cell line (production host): CHO-K1 / Production host: CRICETULUS GRISEUS (Chinese hamster) / References: UniProt: P06276, cholinesterase

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Sugars , 2 types, 6 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpb1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1b_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#7: 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 , 7 types, 201 molecules

#3: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-MF5 / 1-(1-methylpyridin-1-ium-2-yl)-N-[[2,3,4,5,6-pentakis(fluoranyl)phenyl]methoxy]methanimine / methyl2-(pentafluorobenzyloxyimino)pyridinium


Mass: 317.234 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H10F5N2O
#8: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#9: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O

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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: 3.16 Å3/Da / Density % sol: 61 % / Description: NONE
Crystal growpH: 6.5 / Details: 2.1 M AMMONIUM SULFATE, 0.1 M MES BUFFER PH 6.5

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.00407
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 26, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00407 Å / Relative weight: 1
ReflectionResolution: 2.5→30.88 Å / Num. obs: 27807 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 45.8 Å2 / Rmerge(I) obs: 0.01 / Net I/σ(I): 21.4
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.06 / Mean I/σ(I) obs: 3.58 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1P0I

1p0i


Resolution: 2.5→30.878 Å / SU ML: 0.25 / σ(F): 1.36 / Phase error: 22.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.212 1112 4 %
Rwork0.1644 --
obs0.1663 27798 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.98 Å2 / ksol: 0.354 e/Å3
Refinement stepCycle: LAST / Resolution: 2.5→30.878 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4207 0 170 188 4565
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064535
X-RAY DIFFRACTIONf_angle_d1.2596175
X-RAY DIFFRACTIONf_dihedral_angle_d21.0891684
X-RAY DIFFRACTIONf_chiral_restr0.091671
X-RAY DIFFRACTIONf_plane_restr0.005782
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.61370.24611380.19693306X-RAY DIFFRACTION99
2.6137-2.75150.29141380.20713313X-RAY DIFFRACTION100
2.7515-2.92370.24221380.19943322X-RAY DIFFRACTION100
2.9237-3.14930.27791390.1933331X-RAY DIFFRACTION100
3.1493-3.46580.2611400.17533353X-RAY DIFFRACTION100
3.4658-3.96640.20621390.14713324X-RAY DIFFRACTION99
3.9664-4.99390.13781390.12833345X-RAY DIFFRACTION98
4.9939-30.88080.21111410.16843392X-RAY DIFFRACTION95
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)
11.9780.26130.33841.88610.35882.32840.1645-0.49420.10180.4672-0.0819-0.056-0.10360.0094-0.06810.3115-0.0748-0.03630.3797-0.08170.291829.637717.695537.8462
23.70670.00631.35261.8618-0.31773.0680.1511-0.2532-0.32630.4397-0.0796-0.57350.34360.61-0.10930.39710.0071-0.15470.4499-0.05780.497440.81393.23633.1803
33.1868-0.2495-0.50452.33650.94732.27590.01950.22420.1411-0.37370.1141-0.0932-0.27170.1716-0.12570.3271-0.0466-0.05450.2907-0.04570.248432.407819.013912.2258
48.68042.13965.7231.26670.68784.4780.04610.386-0.3821-0.00750.4091-0.08820.13270.3411-0.41920.1944-0.10030.02360.12750.03880.261526.047929.689432.4666
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 3 THROUGH 242)
2X-RAY DIFFRACTION2CHAIN A AND (RESID 243 THROUGH 322)
3X-RAY DIFFRACTION3CHAIN A AND (RESID 323 THROUGH 529)
4X-RAY DIFFRACTION4CHAIN A AND (RESID 1178 THROUGH 1178)

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