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- PDB-9ayt: Structure of the quorum quenching lactonase GcL bound to N-hexano... -

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Basic information

Entry
Database: PDB / ID: 9ayt
TitleStructure of the quorum quenching lactonase GcL bound to N-hexanoyl-L-homoserine lactone
ComponentsGcL lactonase
KeywordsHYDROLASE / quorum sensing / quorum quenching / lactonase / metalloenzyme
Function / homology
Function and homology information


hydrolase activity / metal ion binding
Similarity search - Function
: / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
ACETATE ION / : / : / N-[(3S)-2-oxotetrahydrofuran-3-yl]hexanamide / Putative hydrolase
Similarity search - Component
Biological speciesParageobacillus caldoxylosilyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsCorbella, M. / Bravo, J.A. / Demkiv, A.O. / Calixto, A.R. / Sompiyachoke, K. / Bergonzi, C. / Kamerlin, S.C.L. / Elias, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM133487 United States
CitationJournal: Jacs Au / Year: 2024
Title: Catalytic Redundancies and Conformational Plasticity Drives Selectivity and Promiscuity in Quorum Quenching Lactonases.
Authors: Corbella, M. / Bravo, J. / Demkiv, A.O. / Calixto, A.R. / Sompiyachoke, K. / Bergonzi, C. / Brownless, A.R. / Elias, M.H. / Kamerlin, S.C.L.
History
DepositionMar 8, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
P: GcL lactonase
D: GcL lactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,46538
Polymers68,7582
Non-polymers2,70736
Water3,855214
1
P: GcL lactonase
hetero molecules

D: GcL lactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,46538
Polymers68,7582
Non-polymers2,70736
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
2
D: GcL lactonase
hetero molecules

P: GcL lactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,46538
Polymers68,7582
Non-polymers2,70736
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
MethodPISA
Unit cell
Length a, b, c (Å)108.500, 108.500, 228.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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Protein , 1 types, 2 molecules PD

#1: Protein GcL lactonase


Mass: 34378.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parageobacillus caldoxylosilyticus (bacteria)
Gene: GCA01S_030_00190 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A023DFE8

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Non-polymers , 8 types, 250 molecules

#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-HL6 / N-[(3S)-2-oxotetrahydrofuran-3-yl]hexanamide / N-hexanoyl-L-homoserine lactone


Mass: 199.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17NO3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#8: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.76 Å3/Da / Density % sol: 67.33 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 1.0 - 1.25 M ammonium sulfate and 0.1 M sodium acetate pH 4.0 - 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033199 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033199 Å / Relative weight: 1
ReflectionResolution: 2.1→76.17 Å / Num. obs: 58454 / % possible obs: 99.8 % / Redundancy: 6.25 % / CC1/2: 0.996 / Net I/σ(I): 9.75
Reflection shellResolution: 2.1→2.2 Å / Mean I/σ(I) obs: 2.33 / Num. unique obs: 7610 / CC1/2: 0.853

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→76.17 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.44 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22039 2923 5 %RANDOM
Rwork0.19218 ---
obs0.19358 55531 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.558 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.1→76.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4492 0 166 214 4872
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0124947
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164544
X-RAY DIFFRACTIONr_angle_refined_deg0.6871.8396676
X-RAY DIFFRACTIONr_angle_other_deg0.2761.77910483
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4955587
X-RAY DIFFRACTIONr_dihedral_angle_2_deg2.181528
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.74410812
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.2350.2676
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025899
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021153
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_it3.9054.0192324
X-RAY DIFFRACTIONr_mcbond_other3.9054.0212325
X-RAY DIFFRACTIONr_mcangle_it4.7717.22913
X-RAY DIFFRACTIONr_mcangle_other4.7737.2012914
X-RAY DIFFRACTIONr_scbond_it5.2694.6982623
X-RAY DIFFRACTIONr_scbond_other5.2544.692616
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.6038.2673752
X-RAY DIFFRACTIONr_long_range_B_refined8.80640.435307
X-RAY DIFFRACTIONr_long_range_B_other8.80540.435308
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 214 -
Rwork0.363 4075 -
obs--99.91 %

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