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- PDB-9b2o: Structure of the quorum quenching lactonase GcL bound to the hydr... -

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Basic information

Entry
Database: PDB / ID: 9b2o
TitleStructure of the quorum quenching lactonase GcL bound to the hydrolysis product of N-octanoyl-L-homoserine lactone
ComponentsGcL lactonase
KeywordsHYDROLASE/PRODUCT / quorum sensing / quorum quenching / lactonase / metalloenzyme / HYDROLASE / HYDROLASE-PRODUCT complex
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
: / : / : / Putative hydrolase
Similarity search - Component
Biological speciesParageobacillus caldoxylosilyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 15, 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
X: GcL lactonase
F: GcL lactonase
L: GcL lactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,69717
Polymers103,1373
Non-polymers1,56114
Water6,521362
1
X: GcL lactonase
F: GcL lactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,86212
Polymers68,7582
Non-polymers1,10410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-127 kcal/mol
Surface area23070 Å2
MethodPISA
2
L: GcL lactonase
hetero molecules

L: GcL lactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,67010
Polymers68,7582
Non-polymers9128
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4760 Å2
ΔGint-107 kcal/mol
Surface area23080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.360, 109.810, 97.370
Angle α, β, γ (deg.)90.00, 116.35, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11L-411-

HOH

21L-435-

HOH

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Components

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Protein , 1 types, 3 molecules XFL

#1: Protein GcL lactonase


Mass: 34378.914 Da / Num. of mol.: 3
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 , 5 types, 376 molecules

#2: Chemical ChemComp-A1AI3 / N-octanoyl-L-homoserine


Mass: 245.315 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H23NO4
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / 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: 3.75 Å3/Da / Density % sol: 67.18 %
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-D / Wavelength: 1.03321 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03321 Å / Relative weight: 1
ReflectionResolution: 1.85→74.13 Å / Num. obs: 124206 / % possible obs: 95.8 % / Redundancy: 4.62 % / CC1/2: 0.999 / Net I/σ(I): 14.19
Reflection shellResolution: 1.85→1.95 Å / Num. unique obs: 17767 / CC1/2: 0.927

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Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→74.13 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.134 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21475 6211 5 %RANDOM
Rwork0.18674 ---
obs0.18814 117995 95.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.042 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0.01 Å2
2---0 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.85→74.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6711 0 82 362 7155
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0136968
X-RAY DIFFRACTIONr_bond_other_d0.0040.0176366
X-RAY DIFFRACTIONr_angle_refined_deg1.7021.6479450
X-RAY DIFFRACTIONr_angle_other_deg1.5031.59514661
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0795825
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.25622.576396
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.483151143
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5851542
X-RAY DIFFRACTIONr_chiral_restr0.0810.2879
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027956
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021668
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_it3.4213.9653318
X-RAY DIFFRACTIONr_mcbond_other3.43.9643317
X-RAY DIFFRACTIONr_mcangle_it4.165.9264137
X-RAY DIFFRACTIONr_mcangle_other4.165.9274138
X-RAY DIFFRACTIONr_scbond_it5.5494.6253650
X-RAY DIFFRACTIONr_scbond_other5.5274.6213646
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.8756.695308
X-RAY DIFFRACTIONr_long_range_B_refined945.4517629
X-RAY DIFFRACTIONr_long_range_B_other9.01345.3447584
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 448 -
Rwork0.332 8510 -
obs--94.18 %

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