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- PDB-8qzu: XhpG hydrolase mutant S98A of Xenorhabdus hominickii -

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Basic information

Entry
Database: PDB / ID: 8qzu
TitleXhpG hydrolase mutant S98A of Xenorhabdus hominickii
ComponentsCarboxylesterase
KeywordsBIOSYNTHETIC PROTEIN / alpha/beta hydrolase / post-NRPS enzyme / tailoring enzyme / oxopyrrolizidinacetamide hydrolase
Function / homology: / carboxylesterase / carboxylesterase activity / Alpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / ACETATE ION / Carboxylesterase
Function and homology information
Biological speciesXenorhabdus hominickii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 Å
AuthorsCalderari, A. / Gruez, A. / Weissman, K.J.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-20-CE92-0038 France
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2024
Title: Pyrrolizwilline, a Unique Bacterial Alkaloid Assembled by a Nonribosomal Peptide Synthetase and non-Enzymatic Dimerization.
Authors: Effert, J. / Westphalen, M. / Calderari, A. / Shi, Y.M. / Elamri, I. / Najah, S. / Grun, P. / Li, Y. / Gruez, A. / Weissman, K.J. / Bode, H.B.
History
DepositionOct 30, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 2.0Dec 18, 2024Group: Database references / Polymer sequence / Category: citation / citation_author / entity_poly
Item: _citation.journal_volume / _citation.title ..._citation.journal_volume / _citation.title / _citation_author.identifier_ORCID / _entity_poly.pdbx_target_identifier

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carboxylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4182
Polymers29,3591
Non-polymers591
Water4,107228
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.830, 68.540, 75.480
Angle α, β, γ (deg.)90.00, 98.11, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Carboxylesterase / Oxopyrrolizidinacetamide hydrolase


Mass: 29359.439 Da / Num. of mol.: 1 / Mutation: S98A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenorhabdus hominickii (bacteria) / Strain: ANU1 / Gene: Xhom_00310 / Plasmid: pBG102 / Details (production host): SUMO-His6 tag / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2G0QDP0
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.13 Å3/Da / Density % sol: 42.24 % / Description: prismatic
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 8K, 200mM Magnesium acetate, 100mM sodium Cacodylate
PH range: 5.5-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.82656 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 28, 2022
RadiationMonochromator: channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82656 Å / Relative weight: 1
ReflectionResolution: 1.18→39.5 Å / Num. obs: 78411 / % possible obs: 98 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.017 / Rrim(I) all: 0.044 / Χ2: 0.95 / Net I/σ(I): 17.9 / Num. measured all: 541333
Reflection shellResolution: 1.18→1.21 Å / % possible obs: 92.7 % / Redundancy: 6.4 % / Rmerge(I) obs: 1.48 / Num. measured all: 34900 / Num. unique obs: 5480 / CC1/2: 0.674 / Rpim(I) all: 0.625 / Rrim(I) all: 1.611 / Χ2: 0.9 / Net I/σ(I) obs: 1.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.18→20 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.186 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.19625 3920 5 %RANDOM
Rwork0.1663 ---
obs0.16778 74471 97.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.582 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å2-0 Å2-1.18 Å2
2---0.89 Å2-0 Å2
3---2.09 Å2
Refinement stepCycle: 1 / Resolution: 1.18→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2035 0 4 231 2270
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0122081
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161890
X-RAY DIFFRACTIONr_angle_refined_deg1.7371.6342822
X-RAY DIFFRACTIONr_angle_other_deg0.5841.5574364
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2715269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.673516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.71610326
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0910.2331
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022353
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02393
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_it1.8421.7811071
X-RAY DIFFRACTIONr_mcbond_other1.8481.7811070
X-RAY DIFFRACTIONr_mcangle_it2.2073.2041338
X-RAY DIFFRACTIONr_mcangle_other2.3383.2111339
X-RAY DIFFRACTIONr_scbond_it3.1512.1151010
X-RAY DIFFRACTIONr_scbond_other3.152.1161011
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7353.7141484
X-RAY DIFFRACTIONr_long_range_B_refined3.49519.722381
X-RAY DIFFRACTIONr_long_range_B_other3.43518.532321
X-RAY DIFFRACTIONr_rigid_bond_restr9.53233971
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.183→1.214 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.548 273 -
Rwork0.531 5183 -
obs--92.58 %

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