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- PDB-5ch5: E3 alpha-esterase-7 carboxylesterase -

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Basic information

Entry
Database: PDB / ID: 5ch5
TitleE3 alpha-esterase-7 carboxylesterase
ComponentsCarboxylic ester hydrolase
KeywordsHYDROLASE / Carboxylesterase / OP-hydrolase / organophosphates / structural dynamics
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / carboxylic ester hydrolase activity
Similarity search - Function
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
DIETHYL HYDROGEN PHOSPHATE / Carboxylic ester hydrolase
Similarity search - Component
Biological speciesLucilia cuprina (Australian sheep blowfly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsCorrey, G. / Mabbitt, P. / Jackson, C.J.
CitationJournal: Structure / Year: 2016
Title: Mapping the Accessible Conformational Landscape of an Insect Carboxylesterase Using Conformational Ensemble Analysis and Kinetic Crystallography.
Authors: Correy, G.J. / Carr, P.D. / Meirelles, T. / Mabbitt, P.D. / Fraser, N.J. / Weik, M. / Jackson, C.J.
History
DepositionJul 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carboxylic ester hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5432
Polymers66,3891
Non-polymers1541
Water7,026390
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.816, 101.254, 225.818
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-741-

HOH

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Components

#1: Protein Carboxylic ester hydrolase


Mass: 66388.836 Da / Num. of mol.: 1 / Mutation: D83A, M364L, I419F, A472T, I505T, K530E, D554G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lucilia cuprina (Australian sheep blowfly)
Gene: LcaE7 / Production host: Escherichia coli (E. coli)
References: UniProt: Q25252, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Chemical ChemComp-DPF / DIETHYL HYDROGEN PHOSPHATE


Mass: 154.102 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H11O4P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / 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: 2.26 Å3/Da / Density % sol: 45.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 20% PEG 2K MME, 100 mM sodium acetate pH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.8266 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8266 Å / Relative weight: 1
ReflectionResolution: 1.53→46.2 Å / Num. obs: 85388 / % possible obs: 100 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.146 / Net I/σ(I): 11.6
Reflection shellResolution: 1.53→1.56 Å / Redundancy: 12 % / Rmerge(I) obs: 1.79 / Mean I/σ(I) obs: 1.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FNG

4fng


Resolution: 1.53→46.2 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.248 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23773 4499 5 %RANDOM
Rwork0.19804 ---
obs0.20001 85388 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.536 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å2-0 Å2-0 Å2
2--0.97 Å20 Å2
3----0.79 Å2
Refinement stepCycle: LAST / Resolution: 1.53→46.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4557 0 8 390 4955
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0194717
X-RAY DIFFRACTIONr_bond_other_d0.0080.024433
X-RAY DIFFRACTIONr_angle_refined_deg1.9321.9576385
X-RAY DIFFRACTIONr_angle_other_deg1.1553.00110239
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4595573
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.29724.35223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.36915830
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4261525
X-RAY DIFFRACTIONr_chiral_restr0.1320.2679
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0215329
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021094
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_it1.4861.6362283
X-RAY DIFFRACTIONr_mcbond_other1.4841.6362282
X-RAY DIFFRACTIONr_mcangle_it2.042.4542859
X-RAY DIFFRACTIONr_mcangle_other2.0412.4542860
X-RAY DIFFRACTIONr_scbond_it2.4591.9252434
X-RAY DIFFRACTIONr_scbond_other2.4591.9252435
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7232.7773527
X-RAY DIFFRACTIONr_long_range_B_refined4.93614.0425694
X-RAY DIFFRACTIONr_long_range_B_other4.89113.8425566
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.53→1.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 300 -
Rwork0.304 6279 -
obs--100 %

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