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- PDB-9hgz: Crystal structure of recombinant swine butyrylcholinesterase -

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Basic information

Entry
Database: PDB / ID: 9hgz
TitleCrystal structure of recombinant swine butyrylcholinesterase
ComponentsCarboxylic ester hydrolase
KeywordsHYDROLASE / Butyrylcholinesterase / swine / recombinant
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / cholinesterase activity / extracellular region
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 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Carboxylic ester hydrolase
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsBrazzolotto, X. / Nachon, F.
Funding support France, 1items
OrganizationGrant numberCountry
French Ministry of Armed ForcesNBC-5-C-2316 France
CitationJournal: To Be Published
Title: Crystal structure of recombinant swine butyrylcholinesterase
Authors: Brazzolotto, X. / Nachon, F.
History
DepositionNov 20, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carboxylic ester hydrolase
B: Carboxylic ester hydrolase
C: Carboxylic ester hydrolase
D: Carboxylic ester hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,10346
Polymers239,5124
Non-polymers7,59142
Water8,359464
1
A: Carboxylic ester hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,48914
Polymers59,8781
Non-polymers2,61113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carboxylic ester hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,94716
Polymers59,8781
Non-polymers2,06915
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Carboxylic ester hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,26712
Polymers59,8781
Non-polymers2,38911
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Carboxylic ester hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3994
Polymers59,8781
Non-polymers5223
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.553, 124.553, 175.706
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Space group name HallP4w
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: -x,-y,z+1/2

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Carboxylic ester hydrolase


Mass: 59877.926 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Maturated protein (no signal peptide) Devoid of the C-terminal part (STOP codon at residue 530)
Source: (gene. exp.) Sus scrofa (pig) / Gene: BCHE / Production host: Drosophila melanogaster (fruit fly)
References: UniProt: A0A4X1VEU5, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases

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Sugars , 5 types, 12 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-4/a4-b1_a6-e1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: 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 genetically manipulated 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
#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#6: 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.: 6 / Source method: obtained synthetically / 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 , 6 types, 494 molecules

#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#9: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#10: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#11: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 464 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.85 Å3/Da / Density % sol: 56.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MAR CCD 300 mm / Detector: CCD / Date: Nov 27, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.458→124.6 Å / Num. obs: 97104 / % possible obs: 100 % / Redundancy: 14 % / Biso Wilson estimate: 34.18 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.308 / Rpim(I) all: 0.085 / Rrim(I) all: 0.32 / Net I/σ(I): 11.454
Reflection shellResolution: 2.458→2.5 Å / Redundancy: 9.44 % / Rmerge(I) obs: 2.109 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4836 / CC1/2: 0.336 / Rpim(I) all: 0.716 / Rrim(I) all: 2.228 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MxCuBEdata collection
autoPROCdata processing
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
PHENIX1.21.2_5419refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.46→124.55 Å / SU ML: 0.2885 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.9266
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2346 4837 4.98 %
Rwork0.2033 92214 -
obs0.2049 97051 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.33 Å2
Refinement stepCycle: LAST / Resolution: 2.46→124.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16395 0 483 464 17342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002717318
X-RAY DIFFRACTIONf_angle_d0.569623453
X-RAY DIFFRACTIONf_chiral_restr0.04392544
X-RAY DIFFRACTIONf_plane_restr0.00452979
X-RAY DIFFRACTIONf_dihedral_angle_d15.26966657
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.46-2.490.28161720.29773044X-RAY DIFFRACTION99.47
2.49-2.510.31871270.29793090X-RAY DIFFRACTION99.6
2.51-2.550.31591680.2793044X-RAY DIFFRACTION99.88
2.55-2.580.27671700.27873028X-RAY DIFFRACTION99.94
2.58-2.610.26771670.28043070X-RAY DIFFRACTION99.72
2.61-2.650.32971570.28163077X-RAY DIFFRACTION99.78
2.65-2.690.37141390.27943069X-RAY DIFFRACTION99.91
2.69-2.730.33411520.27623088X-RAY DIFFRACTION99.91
2.73-2.770.29431570.25363104X-RAY DIFFRACTION99.88
2.77-2.810.29641630.23983025X-RAY DIFFRACTION99.94
2.81-2.860.26581740.23653033X-RAY DIFFRACTION99.91
2.86-2.910.28821840.23653093X-RAY DIFFRACTION99.97
2.91-2.970.24581750.22873029X-RAY DIFFRACTION99.97
2.97-3.030.25611820.23143095X-RAY DIFFRACTION100
3.03-3.10.28461870.2343004X-RAY DIFFRACTION100
3.1-3.170.25661410.23243104X-RAY DIFFRACTION99.97
3.17-3.250.27421600.22313049X-RAY DIFFRACTION100
3.25-3.340.26581580.21733080X-RAY DIFFRACTION100
3.34-3.430.23441790.21323046X-RAY DIFFRACTION99.91
3.43-3.540.25051400.19473119X-RAY DIFFRACTION100
3.54-3.670.23321740.18533059X-RAY DIFFRACTION100
3.67-3.820.22131540.17653089X-RAY DIFFRACTION100
3.82-3.990.18151430.17213097X-RAY DIFFRACTION100
3.99-4.20.20871600.16083070X-RAY DIFFRACTION100
4.2-4.470.16371500.14943101X-RAY DIFFRACTION100
4.47-4.810.17141710.14843070X-RAY DIFFRACTION99.97
4.81-5.290.20371530.16453105X-RAY DIFFRACTION99.97
5.3-6.060.20531550.17483105X-RAY DIFFRACTION100
6.06-7.640.23031480.19183110X-RAY DIFFRACTION100
7.64-124.550.17221770.1763117X-RAY DIFFRACTION99.46
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)
10.0982477470695-0.0639053213076-0.04202263657750.1610608248160.07499775907250.07720297588490.007862613789680.074504702910.0107560213907-0.1051860395240.009408808987590.0364236697009-0.0336671380913-0.03658100642880.006752180294290.1219711682310.03324684835070.006377714012940.2089054174270.01336025740780.125461299329-11.707459078224.86449985928.04317940439
20.0887022656006-0.0299921650357-0.06450919093820.05903363439070.01286008257980.07173263941720.000870536800101-0.0760934102967-0.0437010057219-0.0352620324298-0.0854150441814-0.0681312205281-0.02886422349880.0926352393584-0.074508211858-0.04234174376670.07251639112580.0006811509104480.227028059724-0.01050125067380.19146979007-40.191761241445.395173926432.6368277303
30.2580638481810.164066013481-0.00283510025370.116845667056-0.003904014472130.1528032397870.06460065362630.390107933148-0.1344124289460.03850347595050.1271325561740.058366185047-0.0412993677242-0.3024990197320.24226258158-0.0804353345719-0.102170215734-0.04247333634070.5149760365640.030363496430.179827594407-85.587066324547.694457945544.3271873543
40.04448656946740.0271966655810.008188014688570.05336277762040.03466727384670.01094208578380.02057741644310.0284299830281-0.1473987024780.184268087207-0.06014339792080.2092598127670.216817676008-0.122759534831-0.003644570817030.415825182434-0.443180216690.08054037931410.0933802877798-0.1137767294760.365494337434-19.3971669412-19.6909381927-4.62689030107
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Label seq-ID: 1

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
11chain 'A'AA - N4 - 542
22chain 'B'BO - X3 - 538
33chain 'C'CY - KA4 - 541
44chain 'D'DLA - OA10 - 532

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