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- PDB-5fpp: Structure of a pre-reaction ternary complex between sarin- acetyl... -

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Basic information

Entry
Database: PDB / ID: 5fpp
TitleStructure of a pre-reaction ternary complex between sarin- acetylcholinesterase and HI-6
ComponentsACETYLCHOLINESTERASE
KeywordsHYDROLASE / SARIN / HI-6 / QM / DENSITY FUNCTIONAL THEORY CALCULATIONS / MICHAELIS COMPLEX.
Function / homology
Function and homology information


acetylcholine metabolic process / serine hydrolase activity / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / positive regulation of dendrite morphogenesis / acetylcholine receptor signaling pathway / choline metabolic process / osteoblast development ...acetylcholine metabolic process / serine hydrolase activity / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / positive regulation of dendrite morphogenesis / acetylcholine receptor signaling pathway / choline metabolic process / osteoblast development / acetylcholinesterase activity / positive regulation of axonogenesis / basement membrane / regulation of receptor recycling / synaptic cleft / side of membrane / laminin binding / collagen binding / synapse assembly / response to insulin / neuromuscular junction / receptor internalization / nuclear envelope / positive regulation of cold-induced thermogenesis / retina development in camera-type eye / presynaptic membrane / postsynaptic membrane / cell adhesion / endoplasmic reticulum lumen / axon / neuronal cell body / dendrite / synapse / perinuclear region of cytoplasm / Golgi apparatus / cell surface / protein homodimerization activity / extracellular space / identical protein binding / plasma membrane
Similarity search - Function
Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / : / 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 ...Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / : / 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
2-(2-ETHOXYETHOXY)ETHANOL / CARBONATE ION / Chem-HI6 / Acetylcholinesterase
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsAllgardsson, A. / Berg, L. / Akfur, C. / Hornberg, A. / Worek, F. / Linusson, A. / Ekstrom, F.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structure of a Prereaction Complex between the Nerve Agent Sarin, its Biological Target Acetylcholinesterase, and the Antidote Hi-6.
Authors: Allgardsson, A. / Berg, L. / Akfur, C. / Hornberg, A. / Worek, F. / Linusson, A. / Ekstrom, F.J.
History
DepositionDec 2, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
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_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4May 12, 2021Group: Derived calculations / Structure summary
Category: chem_comp / pdbx_struct_assembly ...chem_comp / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _chem_comp.pdbx_synonyms
Revision 1.5Jan 10, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ACETYLCHOLINESTERASE
B: ACETYLCHOLINESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,17710
Polymers120,7082
Non-polymers1,4698
Water8,233457
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint19 kcal/mol
Surface area38000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.825, 111.552, 227.556
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 3 molecules AB

#1: Protein ACETYLCHOLINESTERASE / ACHE


Mass: 60354.070 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, UNP RESIDUES 32-574
Source method: isolated from a genetically manipulated source
Details: SARIN PHOSPHONYLATION PRODUCT COVALENTLY ATTACHED TO SER203
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell line (production host): HEK293F / Production host: HOMO SAPIENS (human) / References: UniProt: P21836, 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.: 1
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 , 5 types, 464 molecules

#3: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO3
#4: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#5: Chemical ChemComp-AE3 / 2-(2-ETHOXYETHOXY)ETHANOL


Mass: 134.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O3
#6: Chemical ChemComp-HI6 / 4-(AMINOCARBONYL)-1-[({2-[(E)-(HYDROXYIMINO)METHYL]PYRIDINIUM-1-YL}METHOXY)METHYL]PYRIDINIUM / 1-(2-HYDROXY-IMINOMETHYLPYRIDINIUM)-1-(4-CARBOXYAMINO)-PYRIDINIUM DIMETHYLETHER


Mass: 288.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H16N4O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 457 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.14 Å3/Da / Density % sol: 70.32 % / Description: NONE
Crystal growpH: 7 / Details: pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1.039
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.039 Å / Relative weight: 1
ReflectionResolution: 2.4→29 Å / Num. obs: 77695 / % possible obs: 98.1 % / Observed criterion σ(I): 2.7 / Redundancy: 3.2 % / Biso Wilson estimate: 48.86 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.1
Reflection shellHighest resolution: 2.4 Å / Redundancy: 2 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.7 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J06

1j06


Resolution: 2.4→28.95 Å / SU ML: 0.32 / σ(F): 1.34 / Phase error: 23 / Stereochemistry target values: ML
Details: SOME REGIONS OF THE CATALYTIC SITE IS DISORDERED. THE REFINEMENT INCLUDED AN INTEGRATED METHODOLOGY CYCLING BETWEEN A CONVENTIONAL CRYSTALLOGRAPHIC REFINEMENT AND A QUANTUM CHEMICAL CLUSTER ...Details: SOME REGIONS OF THE CATALYTIC SITE IS DISORDERED. THE REFINEMENT INCLUDED AN INTEGRATED METHODOLOGY CYCLING BETWEEN A CONVENTIONAL CRYSTALLOGRAPHIC REFINEMENT AND A QUANTUM CHEMICAL CLUSTER APPROACH USING IMPLICIT DISPERSION- CORRECTED DENSITY FUNCTIONAL THEORY (DFT) CALCULATIONS
RfactorNum. reflection% reflection
Rfree0.2133 1541 2 %
Rwork0.1756 --
obs0.1763 77689 98.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→28.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8369 0 98 457 8924
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088867
X-RAY DIFFRACTIONf_angle_d1.10312100
X-RAY DIFFRACTIONf_dihedral_angle_d15.9613222
X-RAY DIFFRACTIONf_chiral_restr0.0761286
X-RAY DIFFRACTIONf_plane_restr0.0051597
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.47740.33211230.27326793X-RAY DIFFRACTION97
2.4774-2.56590.27231440.23926812X-RAY DIFFRACTION98
2.5659-2.66860.27771510.22436878X-RAY DIFFRACTION99
2.6686-2.78990.27181410.21996923X-RAY DIFFRACTION99
2.7899-2.93690.28791400.21826900X-RAY DIFFRACTION99
2.9369-3.12070.2511540.21296929X-RAY DIFFRACTION99
3.1207-3.36130.24251320.19586943X-RAY DIFFRACTION99
3.3613-3.6990.21451390.17416969X-RAY DIFFRACTION99
3.699-4.23280.18291340.14776926X-RAY DIFFRACTION98
4.2328-5.32750.16531410.13116996X-RAY DIFFRACTION97
5.3275-28.9520.18141420.16217079X-RAY DIFFRACTION96
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)
11.38840.0965-0.40261.4015-0.21513.0163-0.0621-0.10130.05810.20880.05450.01010.0917-0.03210.01380.26390.0042-0.02570.21730.0430.22330.871711.235929.1061
25.67411.48050.43981.2384-0.00642.2876-0.19260.383-0.2237-0.12040.0683-0.21830.32780.3210.11340.33070.05820.02740.24860.02680.237240.37039.472510.3067
31.09080.0951-0.20181.1775-0.73974.07830.02930.11640.0214-0.04130.03630.1892-0.0771-0.4659-0.06750.1963-0.0209-0.04270.29170.01240.267418.403517.16426.4542
43.8619-0.65721.87788.0186-1.33873.197-0.0649-0.0944-0.68480.26260.12730.90490.5871-1.22170.09080.4297-0.27210.0010.60.08190.56.97390.979313.7388
53.5322-2.2915-0.76652.67922.35237.11680.15350.594-0.2056-0.3554-0.27970.2213-0.1152-0.04330.11520.3757-0.0629-0.09990.32320.06930.275420.35676.5767-2.0484
65.6968-1.1688-1.96212.02920.67896.23940.06670.55190.0424-0.2481-0.1570.3111-0.1522-0.76180.05280.36110.0233-0.09840.3881-0.13830.3375-3.38286.347-61.6128
71.3612-0.11840.17121.59440.54563.61530.11640.126-0.1948-0.0951-0.12810.18940.4578-0.2331-0.00010.3324-0.0153-0.06520.3331-0.0890.27792.31611.5916-51.7302
84.7418-6.32313.66638.4533-3.92543.98420.21390.15490.0171-0.2873-0.101-0.1936-0.23580.4092-0.09290.3733-0.0033-0.03740.4063-0.07580.252914.09648.924-55.736
92.3638-1.3846-0.11033.20791.30693.29610.09470.0389-0.14690.11390.0847-0.24890.43990.5313-0.16610.33420.0475-0.06050.3623-0.04570.249318.10551.4204-45.1536
105.1128-1.5874-1.77581.56162.19525.02970.25990.08380.71780.00370.0653-0.5209-0.50010.6874-0.30790.2899-0.0223-0.0950.4019-0.04790.371818.592114.8574-39.8306
117.41562.00910.30875.2243-1.0112.68970.3441-0.018-0.71740.218-0.0276-0.08130.94750.1173-0.33140.69220.0109-0.09240.2904-0.01930.32313.8477-6.1588-22.0526
122.4513-0.40921.34272.1835-0.77973.9890.2227-0.2085-0.21120.2218-0.09060.3080.2664-0.3866-0.14860.3401-0.07050.01360.3072-0.10440.28480.56526.0966-29.4041
135.61162.2672.02958.977-2.70042.6601-0.0803-0.52010.9030.16080.11690.9942-0.3886-0.4547-0.010.45370.04620.0210.3507-0.12310.368-1.279922.6124-28.7967
149.1329-1.15445.0581.9414-0.43084.7414-0.02040.1725-0.39690.26610.0161-0.04150.11280.51710.01760.4141-0.05860.00060.3668-0.01330.181713.609411.2404-21.7206
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESSEQ 1:228)
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESSEQ 229:331)
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESSEQ 332:486)
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESSEQ 487:513)
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESSEQ 514:548)
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESSEQ 5:45)
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESSEQ 46:158)
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESSEQ 159:191)
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESSEQ 192:298)
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESSEQ 299:331)
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESSEQ 332:382)
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESSEQ 383:486)
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESSEQ 487:513)
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESSEQ 514:544)

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