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- PDB-3o9m: Co-crystallization studies of full length recombinant BChE with c... -

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Basic information

Entry
Database: PDB / ID: 3o9m
TitleCo-crystallization studies of full length recombinant BChE with cocaine offers insights into cocaine detoxification
ComponentsCholinesterase
KeywordsHYDROLASE / Cholinesterase
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 / hydrolase activity, acting on ester bonds / peptide hormone processing / 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
BENZOIC ACID / Cholinesterase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å
AuthorsAsojo, O.A. / Ngamelue, M.N. / Homma, K. / Lockridge, O.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Cocrystallization studies of full-length recombinant butyrylcholinesterase (BChE) with cocaine.
Authors: Asojo, O.A. / Ngamelue, M.N. / Homma, K. / Lockridge, O.
History
DepositionAug 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cholinesterase
B: Cholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,5434
Polymers130,2992
Non-polymers2442
Water362
1
A: Cholinesterase
hetero molecules

A: Cholinesterase
hetero molecules

A: Cholinesterase
hetero molecules

A: Cholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)261,0868
Polymers260,5984
Non-polymers4884
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
2
B: Cholinesterase
hetero molecules

B: Cholinesterase
hetero molecules

B: Cholinesterase
hetero molecules

B: Cholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)261,0868
Polymers260,5984
Non-polymers4884
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
3
A: Cholinesterase
B: Cholinesterase
hetero molecules

A: Cholinesterase
B: Cholinesterase
hetero molecules

A: Cholinesterase
B: Cholinesterase
hetero molecules

A: Cholinesterase
B: Cholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)522,17316
Polymers521,1968
Non-polymers9778
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area29450 Å2
ΔGint-37 kcal/mol
Surface area156350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.392, 150.392, 142.448
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A-99999 - 99999
2111B-99999 - 99999

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Components

#1: Protein Cholinesterase / Acylcholine acylhydrolase / Choline esterase II / Butyrylcholine esterase / Pseudocholinesterase


Mass: 65149.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCHE, CHE1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P06276, cholinesterase
#2: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.09 Å3/Da / Density % sol: 60.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.98→31.7 Å / Num. obs: 34043 / % possible obs: 99.6 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3
Reflection shellResolution: 2.98→3.3 Å / % possible all: 99.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.98→142.45 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.881 / SU B: 14.761 / SU ML: 0.284 / Cross valid method: THROUGHOUT / ESU R Free: 0.408 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26232 1720 5.1 %RANDOM
Rwork0.22326 ---
obs0.2252 32219 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 55.346 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.98→142.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8452 0 18 2 8472
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0228714
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7611.94511834
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0151060
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.55624.089406
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.29151412
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4871544
X-RAY DIFFRACTIONr_chiral_restr0.1210.21254
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216732
X-RAY DIFFRACTIONr_gen_planes_other
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_mcbond_it0.7991.55286
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.55128528
X-RAY DIFFRACTIONr_scbond_it1.9133428
X-RAY DIFFRACTIONr_scangle_it3.314.53306
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 4236 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.090.05
tight thermal0.140.5
LS refinement shellResolution: 2.979→3.056 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 121 -
Rwork0.229 2336 -
obs--99.64 %

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