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- PDB-2dfp: X-RAY STRUCTURE OF AGED DI-ISOPROPYL-PHOSPHORO-FLUORIDATE (DFP) B... -

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Basic information

Entry
Database: PDB / ID: 2dfp
TitleX-RAY STRUCTURE OF AGED DI-ISOPROPYL-PHOSPHORO-FLUORIDATE (DFP) BOUND TO ACETYLCHOLINESTERASE
ComponentsPROTEIN (ACETYLCHOLINESTERASE)
KeywordsHYDROLASE / AGED ORGANOPHOSPHATE / DFP / SERINE HYDROLASE / NEUROTRANSMITTER CLEAVAGE / CATALYTIC TRIAD / ALPHA/BETA HYDROLASE
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 / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKryger, G. / Millard, C.B. / Silman, I. / Sussman, J.L.
Citation
Journal: Biochemistry / Year: 1999
Title: Crystal structures of aged phosphonylated acetylcholinesterase: nerve agent reaction products at the atomic level.
Authors: Millard, C.B. / Kryger, G. / Ordentlich, A. / Greenblatt, H.M. / Harel, M. / Raves, M.L. / Segall, Y. / Barak, D. / Shafferman, A. / Silman, I. / Sussman, J.L.
#1: 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
DepositionDec 7, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jun 28, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site.occupancy / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_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 2.1Jun 2, 2021Group: Derived calculations / Structure summary / Category: chem_comp / pdbx_struct_oper_list
Item: _chem_comp.pdbx_synonyms / _pdbx_struct_oper_list.matrix[2][1] ..._chem_comp.pdbx_synonyms / _pdbx_struct_oper_list.matrix[2][1] / _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.matrix[3][3] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[2] / _pdbx_struct_oper_list.vector[3]
Revision 2.2Aug 23, 2023Group: 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: PROTEIN (ACETYLCHOLINESTERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8355
Polymers60,5691
Non-polymers1,2654
Water6,774376
1
A: PROTEIN (ACETYLCHOLINESTERASE)
hetero molecules

A: PROTEIN (ACETYLCHOLINESTERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,66910
Polymers121,1392
Non-polymers2,5308
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Unit cell
Length a, b, c (Å)112.636, 112.636, 136.881
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Cell settingtrigonal
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-2116-

HOH

DetailsTORPEDO CALIFONICA ACETYLCHOLINESTERASE IS A G2 DIMER IN SOLUTION (SEE SUSSMAN 1988). THE ASYMMETRIC UNIT CONTAINS A MONOMER, WITH THE CRYSTALLOGRAPHIC TWO-FOLD AXIS RELATING THE TWO MONOMERS IN A DIMER. BIOMOLECULE: THE ENZYME IS A GPI-ANCHORED DIMER, THE TWO MONOMERS IN THE DIMER ARE RELATED BY THE CRYSTALLOGRAPHIC TWO-FOLD SYMMETRY AND THUS GENERATE A FOUR HELIX BUNDLE A365-A375 AND A518-A535. DFP WAS REACTED WITH THE ENZYME IN SOLUTION. THE SOLUTION OF THE INHIBITED ENZYME WAS DIALYZED TO REMOVE EXCESS ORGANOPHOSPHATE, CHECKED FOR ACTIVITY AND FOUND TO REACT LIKE "AGED" PHOSPHYLATED ACHE, AND THEN SUBJECTED TO CRYSTALLIZATION. THIS STRUCTURE IS MORE COMPLETE THAN THE STARTING MODEL OF THE NATIVE STRUCTURE (PDB ID 2ACE). RESIDUES THAT ARE NOT SEEN IN THE CRYSTAL STRUCTURE DUE TO DISORDER INCLUDE THE N-TERMINAL RESIDUE ASP 1 AND THE C-TERMINAL RESIDUES AFTER THR 535. THR 535 IS THE LAST RESIDUE OBSERVED AT THE C-TERMINUS.

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Components

#1: Protein PROTEIN (ACETYLCHOLINESTERASE) / E.C.3.1.1.7


Mass: 60569.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: THE PROTEIN, ACETYLCHOLINESTERASE, WAS TREATED WITH THE ORGANOPHOSPHATE, DFP, PRIOR TO CRYSTALLIZATION.
Source: (natural) Torpedo californica (Pacific electric ray)
Organ: ELECTRIC ORGAN / Variant: G2 FORM / Tissue: ELECTROPLAQUE
Keywords: THE PROTEIN, ACETYLCHOLINESTERASE, WAS TREATED WITH THE ORGANOPHOSPHATE, DFP, PRIOR TO CRYSTALLIZATION
References: UniProt: P04058, acetylcholinesterase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2 / Source method: isolated from a natural source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: isolated from a natural 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
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 376 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsDFP, AGED ORGANOPHOSPHATE MES, USED AS THE CRYSTALLIZATION BUFFER THERE ARE 5 NAG GROUPS NUMBERED ...DFP, AGED ORGANOPHOSPHATE MES, USED AS THE CRYSTALLIZATION BUFFER THERE ARE 5 NAG GROUPS NUMBERED 3001-3005 IN THIS STRUCTURE

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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: 3.8 Å3/Da / Density % sol: 68 % / Description: USED COMPOSITE OMIT MAP METHOD
Crystal growTemperature: 277 K / pH: 5.8 / Details: pH 5.8, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 20011
2MES11
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / PH range low: 6 / PH range high: 5.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
235-40 %(w/v)PEG2001reservoir
30.15 MMES1reservoir
40.05 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: May 15, 1998 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 42208 / Num. obs: 42208 / % possible obs: 93.7 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 45.7 Å2 / Rsym value: 0.05
Reflection shellResolution: 2.3→2.38 Å / % possible all: 65.2
Reflection
*PLUS
Num. obs: 42410 / % possible obs: 94.2 % / Num. measured all: 278106 / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
% possible obs: 66.3 % / Rmerge(I) obs: 0.41

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNS0.4refinement
CNS0.4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ACE

2ace


Resolution: 2.3→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high rms absF: 2409412.92 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1874 4.4 %RANDOM
Rwork0.186 ---
all-42208 --
obs-42208 93.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.45 Å2 / ksol: 0.345 e/Å3
Displacement parametersBiso mean: 42.4 Å2
Baniso -1Baniso -2Baniso -3
1-8.06 Å28.63 Å20 Å2
2--8.06 Å20 Å2
3----16.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.28 Å
Luzzati d res low-4 Å
Luzzati sigma a0.49 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4270 0 82 376 4728
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.31
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.3→2.38 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.363 129 4.5 %
Rwork0.353 2760 -
obs--65.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4DFP.PAR, MES.PARDFP.TOP, MES.TOP
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 40334 / σ(F): 0 / % reflection Rfree: 4.2 % / Rfactor obs: 0.186
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 42.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.31
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shell
*PLUS
Rfactor Rfree: 0.363 / % reflection Rfree: 4.5 % / Rfactor Rwork: 0.353

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