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- PDB-9b2p: Structure of the quorum quenching lactonase GcL D122N mutant - bi... -

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Basic information

Entry
Database: PDB / ID: 9b2p
TitleStructure of the quorum quenching lactonase GcL D122N mutant - bimetallic metal center - C2 space group
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
: / : / Putative hydrolase
Similarity search - Component
Biological speciesParageobacillus caldoxylosilyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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
P: quorum-quenching N-acyl-homoserine lactonase
X: quorum-quenching N-acyl-homoserine lactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,43317
Polymers95,3883
Non-polymers1,04514
Water2,738152
1
X: quorum-quenching N-acyl-homoserine lactonase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)64,20610
Polymers63,5922
Non-polymers6148
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455-x-1/2,y+1/2,-z1
Buried area3650 Å2
ΔGint-118 kcal/mol
Surface area22960 Å2
MethodPISA
2
P: quorum-quenching N-acyl-homoserine lactonase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)64,45414
Polymers63,5922
Non-polymers86212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area3790 Å2
ΔGint-114 kcal/mol
Surface area22580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.770, 109.110, 97.170
Angle α, β, γ (deg.)90.00, 116.42, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11P-418-

HOH

21X-442-

HOH

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Components

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Protein , 1 types, 3 molecules APX

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


Mass: 31796.020 Da / Num. of mol.: 3 / Mutation: D122N
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 , 5 types, 166 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / 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-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Fe
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 3.71 Å3/Da / Density % sol: 66.81 %
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: 1.03333 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03333 Å / Relative weight: 1
ReflectionResolution: 2.25→73.93 Å / Num. obs: 70302 / % possible obs: 98.4 % / Redundancy: 4.08 % / CC1/2: 0.998 / Net I/σ(I): 12.49
Reflection shellResolution: 2.25→2.35 Å / Num. unique obs: 8539 / CC1/2: 0.925

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→73.93 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.37 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23369 3515 5 %RANDOM
Rwork0.20801 ---
obs0.20931 66783 98.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.971 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å2-0 Å20.3 Å2
2--0.08 Å2-0 Å2
3----0.05 Å2
Refinement stepCycle: 1 / Resolution: 2.25→73.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6747 0 3 152 6902
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0010.0126975
X-RAY DIFFRACTIONr_bond_other_d00.0166352
X-RAY DIFFRACTIONr_angle_refined_deg0.6861.8229472
X-RAY DIFFRACTIONr_angle_other_deg0.2441.76814619
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6885833
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.732543
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.432101153
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0340.2982
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.028365
X-RAY DIFFRACTIONr_gen_planes_other00.021687
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_it4.9035.2393326
X-RAY DIFFRACTIONr_mcbond_other4.9045.243326
X-RAY DIFFRACTIONr_mcangle_it6.3639.4194158
X-RAY DIFFRACTIONr_mcangle_other6.3649.4194159
X-RAY DIFFRACTIONr_scbond_it6.635.9363649
X-RAY DIFFRACTIONr_scbond_other6.6175.9343640
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.35410.5545302
X-RAY DIFFRACTIONr_long_range_B_refined11.15651.887666
X-RAY DIFFRACTIONr_long_range_B_other11.16451.917647
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.441 259 -
Rwork0.416 4931 -
obs--98.58 %

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