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- PDB-5ehx: Crystal structure of MSF-aged Torpedo californica Acetylcholinesterase -

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Basic information

Entry
Database: PDB / ID: 5ehx
TitleCrystal structure of MSF-aged Torpedo californica Acetylcholinesterase
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / alpha beta hydrolase / irreversible inhibitor
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
methanesulfonic acid / 3,6,9,12,15-PENTAOXAHEPTADECAN-1-OL / Acetylcholinesterase
Similarity search - Component
Biological speciesTorpedo californica (Pacific electric ray)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPesaresi, A. / Lamba, D.
CitationJournal: To Be Published
Title: Crystal structure of MSF-aged Torpedo californica Acetylcholinesterase
Authors: Pesaresi, A. / Lamba, D.
History
DepositionOct 29, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
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_mod_residue / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_mod_residue.auth_asym_id / _pdbx_struct_mod_residue.auth_seq_id / _pdbx_struct_mod_residue.label_asym_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0May 12, 2021Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / diffrn / pdbx_branch_scheme / pdbx_database_status / pdbx_entity_branch_descriptor / pdbx_entity_instance_feature / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_mod_residue / pdbx_struct_oper_list / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / struct / struct_conn
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_seq_id / _chem_comp.pdbx_synonyms / _citation.title / _diffrn.pdbx_serial_crystal_experiment / _pdbx_branch_scheme.auth_asym_id / _pdbx_branch_scheme.auth_seq_num / _pdbx_database_status.deposit_site / _pdbx_entity_branch_descriptor.descriptor / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value / _pdbx_struct_mod_residue.auth_seq_id / _refine.B_iso_max / _refine.B_iso_min / _refine.details / _refine.ls_wR_factor_R_free / _refine.ls_wR_factor_R_work / _refine.overall_FOM_work_R_set / _refine.overall_SU_R_Cruickshank_DPI / _refine.overall_SU_R_free / _refine_hist.cycle_id / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_residues_total / _refine_ls_shell.R_factor_R_free_error / _refine_ls_shell.number_reflns_all / _reflns.number_all / _reflns.pdbx_Rpim_I_all / _reflns.pdbx_Rrim_I_all / _reflns.pdbx_Rsym_value / _reflns.pdbx_netI_over_av_sigmaI / _reflns.pdbx_number_measured_all / _reflns_shell.number_measured_all / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_Rpim_I_all / _reflns_shell.pdbx_Rrim_I_all / _reflns_shell.pdbx_Rsym_value / _reflns_shell.pdbx_netI_over_sigmaI_obs / _struct.pdbx_CASP_flag / _struct_conn.ptnr2_auth_seq_id
Description: Model orientation/position
Details: Rotation of a Histidine side chain to match with H-bonding network
Provider: author / Type: Coordinate replacement
Revision 3.1Jan 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

Downloads & links

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Assembly

Deposited unit
A: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4236
Polymers60,1941
Non-polymers1,2295
Water4,252236
1
A: Acetylcholinesterase
hetero molecules

A: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,84612
Polymers120,3882
Non-polymers2,45910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_557-x,-x+y,-z+7/31
Buried area4670 Å2
ΔGint8 kcal/mol
Surface area39900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.270, 112.270, 136.840
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Acetylcholinesterase / / AChE


Mass: 60193.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Torpedo californica (Pacific electric ray)
References: UniProt: P04058, acetylcholinesterase

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Sugars , 2 types, 3 molecules

#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.: 1 / Source method: isolated from a natural source / References: acetylcholinesterase
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-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.: 2 / Source method: isolated from a natural source / Formula: C8H15NO6 / References: acetylcholinesterase
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 , 3 types, 238 molecules

#4: Chemical ChemComp-03S / methanesulfonic acid / Methanesulfonic acid


Mass: 96.106 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: CH4O3S / Feature type: SUBJECT OF INVESTIGATION / References: acetylcholinesterase
#5: Chemical ChemComp-AE4 / 3,6,9,12,15-PENTAOXAHEPTADECAN-1-OL


Mass: 266.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O6
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 70.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2 / Details: MES 100 mM, pH 6.2 PEG 200 30%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 10, 2015
RadiationMonochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→48.61 Å / Num. all: 58616 / Num. obs: 58616 / % possible obs: 99.9 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.186 / Rpim(I) all: 0.088 / Rrim(I) all: 0.207 / Rsym value: 0.186 / Net I/av σ(I): 2.3 / Net I/σ(I): 5.3 / Num. measured all: 288894
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.634 / Mean I/σ(I) obs: 1.9 / Num. measured all: 10399 / Num. unique obs: 2024 / Rpim(I) all: 0.069 / Rrim(I) all: 0.161 / Rsym value: 0.145 / Net I/σ(I) obs: 9.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLM7.0.7data reduction
SCALA3.3.2.1data scaling
PHASER2.3.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AE5

1ae5


Resolution: 2.1→48.61 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.251 / WRfactor Rwork: 0.2076 / FOM work R set: 0.8421 / SU B: 3.996 / SU ML: 0.103 / SU R Cruickshank DPI: 0.1479 / SU Rfree: 0.1453 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.237 2956 5 %RANDOM
Rwork0.198 ---
obs0.2 55581 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.76 Å2 / Biso mean: 33.14 Å2 / Biso min: 19.04 Å2
Baniso -1Baniso -2Baniso -3
1-1.04 Å21.04 Å20 Å2
2--1.04 Å20 Å2
3----3.38 Å2
Refinement stepCycle: final / Resolution: 2.1→48.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4245 0 78 236 4559
Biso mean--61.69 35.29 -
Num. residues----532
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0194452
X-RAY DIFFRACTIONr_bond_other_d0.0020.024107
X-RAY DIFFRACTIONr_angle_refined_deg1.9631.9616045
X-RAY DIFFRACTIONr_angle_other_deg0.9663.0039435
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7015531
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.42624.028211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.5815706
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1411524
X-RAY DIFFRACTIONr_chiral_restr0.120.2638
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215032
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021072
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.16 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 190 -
Rwork0.271 4096 -
all-4286 -
obs--99.49 %

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