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- PDB-9b2j: Structure of the quorum quenching lactonase GcL I237M mutant -

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Basic information

Entry
Database: PDB / ID: 9b2j
TitleStructure of the quorum quenching lactonase GcL I237M mutant
Componentsquorum-quenching N-acyl-homoserine 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 / : / : / Putative hydrolase
Similarity search - Component
Biological speciesParageobacillus caldoxylosilyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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

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Assembly

Deposited unit
A: quorum-quenching N-acyl-homoserine lactonase
B: quorum-quenching N-acyl-homoserine lactonase
C: quorum-quenching N-acyl-homoserine lactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,45533
Polymers103,1913
Non-polymers2,26430
Water12,052669
1
A: quorum-quenching N-acyl-homoserine lactonase
hetero molecules

C: quorum-quenching N-acyl-homoserine lactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,18621
Polymers68,7942
Non-polymers1,39219
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556-x+1/2,y+1/2,-z+11
Buried area5250 Å2
ΔGint-145 kcal/mol
Surface area23950 Å2
MethodPISA
2
B: quorum-quenching N-acyl-homoserine lactonase
hetero molecules

B: quorum-quenching N-acyl-homoserine lactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,53724
Polymers68,7942
Non-polymers1,74322
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area5640 Å2
ΔGint-185 kcal/mol
Surface area24490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.400, 110.300, 79.400
Angle α, β, γ (deg.)90.00, 115.90, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein quorum-quenching N-acyl-homoserine lactonase / GcL lactonase


Mass: 34396.953 Da / Num. of mol.: 3 / Mutation: I237M
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, quorum-quenching N-acyl-homoserine lactonase

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Non-polymers , 6 types, 699 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#6: 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
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 669 / 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: 2.81 Å3/Da / Density % sol: 56.28 %
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: 0.99184 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99184 Å / Relative weight: 1
ReflectionResolution: 2.3→64.23 Å / Num. obs: 48202 / % possible obs: 94.9 % / Redundancy: 3.74 % / CC1/2: 0.998 / Net I/σ(I): 19.44
Reflection shellResolution: 2.3→2.4 Å / Num. unique obs: 5605 / CC1/2: 0.975

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→64.17 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.952 / SU B: 6.627 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R: 0.37 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19915 2267 5 %RANDOM
Rwork0.18437 ---
obs0.1851 43062 95.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.759 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-2.83 Å2
2--5.34 Å2-0 Å2
3----1.75 Å2
Refinement stepCycle: 1 / Resolution: 2.35→64.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6706 0 115 669 7490
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0127411
X-RAY DIFFRACTIONr_bond_other_d00.0166694
X-RAY DIFFRACTIONr_angle_refined_deg0.9231.82910098
X-RAY DIFFRACTIONr_angle_other_deg0.3791.77315463
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7855912
X-RAY DIFFRACTIONr_dihedral_angle_2_deg1.1545
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.291101251
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0440.21028
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.029020
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021776
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_it2.7663.4443514
X-RAY DIFFRACTIONr_mcbond_other2.7623.4443512
X-RAY DIFFRACTIONr_mcangle_it4.0066.2264447
X-RAY DIFFRACTIONr_mcangle_other4.0066.2264448
X-RAY DIFFRACTIONr_scbond_it3.4243.8343897
X-RAY DIFFRACTIONr_scbond_other3.4193.833886
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1766.8435627
X-RAY DIFFRACTIONr_long_range_B_refined6.79138.358023
X-RAY DIFFRACTIONr_long_range_B_other6.78338.368021
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.497 162 -
Rwork0.473 3069 -
obs--92.9 %

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