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- PDB-9hh0: Crystal structure of recombinant soman-aged swine butyrylcholines... -

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Basic information

Entry
Database: PDB / ID: 9hh0
TitleCrystal structure of recombinant soman-aged swine butyrylcholinesterase
ComponentsCarboxylic ester hydrolase
KeywordsHYDROLASE / Butyrylcholinesterase / swine / recombinant / organophosphorus compound / aging.
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
METHYLPHOSPHONIC ACID ESTER GROUP / DI(HYDROXYETHYL)ETHER / Carboxylic ester hydrolase
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 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 soman-aged 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)246,87940
Polymers239,5124
Non-polymers7,36836
Water5,837324
1
A: Carboxylic ester hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,65215
Polymers59,8781
Non-polymers2,77414
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carboxylic ester hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,68912
Polymers59,8781
Non-polymers1,81111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Carboxylic ester hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0789
Polymers59,8781
Non-polymers2,2008
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Carboxylic ester hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4604
Polymers59,8781
Non-polymers5823
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.692, 124.692, 175.173
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: Mature protein form (devoid of signal peptide) and devoid of C-terminal part (STOP codon at residue position 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 , 6 types, 13 molecules

#2: 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
#3: 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.: 1
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
#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.: 3
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 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...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: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#6: 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
#7: 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.: 5 / 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, 347 molecules

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


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical
ChemComp-GB / METHYLPHOSPHONIC ACID ESTER GROUP


Mass: 96.022 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH5O3P / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#11: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.84 Å3/Da / Density % sol: 56.73 %
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: Dec 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.66→124.7 Å / Num. obs: 76253 / % possible obs: 99.82 % / Redundancy: 3.9 % / Biso Wilson estimate: 41.58 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.1526 / Rpim(I) all: 0.09052 / Rrim(I) all: 0.1779 / Net I/σ(I): 8.22
Reflection shellResolution: 2.66→2.7 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.311 / Mean I/σ(I) obs: 1.25 / Num. unique obs: 2713 / CC1/2: 0.311 / Rpim(I) all: 0.8235 / Rrim(I) all: 1.556 / % possible all: 97.79

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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: 2.66→124.69 Å / SU ML: 0.3618 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.1903
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2356 3952 5.19 %
Rwork0.1953 72171 -
obs0.1974 76123 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.34 Å2
Refinement stepCycle: LAST / Resolution: 2.66→124.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16576 0 465 324 17365
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002817497
X-RAY DIFFRACTIONf_angle_d0.580223724
X-RAY DIFFRACTIONf_chiral_restr0.04422585
X-RAY DIFFRACTIONf_plane_restr0.00463017
X-RAY DIFFRACTIONf_dihedral_angle_d16.12416766
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.66-2.70.34021500.28532508X-RAY DIFFRACTION97.79
2.7-2.730.31561280.28862556X-RAY DIFFRACTION99.33
2.73-2.770.31761290.28362614X-RAY DIFFRACTION99.64
2.77-2.80.3341450.26762513X-RAY DIFFRACTION99.74
2.8-2.840.29511550.26092580X-RAY DIFFRACTION99.89
2.84-2.890.29651560.26212541X-RAY DIFFRACTION99.78
2.89-2.930.32851550.26122569X-RAY DIFFRACTION99.96
2.93-2.980.29631200.25962594X-RAY DIFFRACTION100
2.98-3.030.3111330.24912592X-RAY DIFFRACTION100
3.03-3.090.31691470.25052526X-RAY DIFFRACTION100
3.09-3.150.27431700.25472577X-RAY DIFFRACTION99.96
3.15-3.210.29181350.24362581X-RAY DIFFRACTION100
3.21-3.280.27441360.23222589X-RAY DIFFRACTION99.96
3.28-3.360.26771360.21722591X-RAY DIFFRACTION100
3.36-3.440.26051320.22052570X-RAY DIFFRACTION99.93
3.44-3.530.28971410.19852573X-RAY DIFFRACTION100
3.53-3.640.22861310.18812583X-RAY DIFFRACTION100
3.64-3.760.2187930.18662641X-RAY DIFFRACTION100
3.76-3.890.22881760.17442550X-RAY DIFFRACTION100
3.89-4.050.2121120.16192598X-RAY DIFFRACTION100
4.05-4.230.17741270.15432624X-RAY DIFFRACTION100
4.23-4.450.17841580.14362562X-RAY DIFFRACTION100
4.45-4.730.19961520.13722554X-RAY DIFFRACTION100
4.73-5.10.18481730.14972562X-RAY DIFFRACTION100
5.1-5.610.22221440.16472597X-RAY DIFFRACTION100
5.61-6.420.20051570.17942577X-RAY DIFFRACTION100
6.42-8.090.18241400.17862603X-RAY DIFFRACTION100
8.09-124.690.17561210.172646X-RAY DIFFRACTION98.86
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)
10.218285057059-0.0988653261736-0.1144101161140.3210925695960.2591226971490.237995780392-0.00804800214480.07905770665150.032974573714-0.08841026818740.02998801478570.0323500966641-0.0318340289855-0.005223112810990.0001564080838260.1638101760110.0208568759905-0.009617912513640.2295143810240.02097259756160.14765471355-11.718036738425.00125050748.19602670701
20.282189556728-0.0848338531441-0.2020822097250.157180936014-0.02372059469870.1722239109910.013935819873-0.0442631856753-0.00154814181253-0.0216056755342-0.0610632714399-0.0192082065818-0.02158647322870.0719260400147-0.0004194945772140.1304597770060.0259569679153-0.01044410590940.234340610324-0.004685791357870.240784504852-40.123238966445.55869930432.4428646124
30.4315458162650.222231083423-0.2182086218070.556397019952-0.08009261081960.269768426410.0167074255910.485300408096-0.1041775847530.1097389786360.16689568684-0.0147185210477-0.0926967833657-0.3389745532780.1910182950730.0126430975267-0.0667220942415-0.01406098114350.5681967113410.0291568935710.211213694355-85.714299190347.902055867544.3118887452
40.1802917804520.0006989827457730.04114866866010.1537422201850.1126049651520.155440145217-0.03812284235560.0859847551482-0.09202333501640.07707399602440.01360563202630.1750444289220.423764224242-0.106529505113-0.01076844384810.482452955732-0.2801927979220.03297383642840.229495536263-0.02300920695490.353273601219-19.4464678149-19.5858512576-4.79503426789
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 - P4 - 544
22chain 'B'BQ - Z3 - 538
33chain 'C'CAA - MA4 - 541
44chain 'D'DNA - QA10 - 532

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