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- PDB-9b2n: Structure of the quorum quenching lactonase GcL D122N mutant - mo... -

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Basic information

Entry
Database: PDB / ID: 9b2n
TitleStructure of the quorum quenching lactonase GcL D122N mutant - monometal center
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: 1.9 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)104,95024
Polymers103,1343
Non-polymers1,81621
Water8,503472
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)69,50511
Polymers68,7562
Non-polymers7499
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556-x+1/2,y+1/2,-z+11
Buried area3890 Å2
ΔGint-104 kcal/mol
Surface area23030 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)70,88926
Polymers68,7562
Non-polymers2,13324
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area6240 Å2
ΔGint-198 kcal/mol
Surface area23770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.360, 109.080, 78.740
Angle α, β, γ (deg.)90.00, 115.95, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-461-

HOH

21B-562-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

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


Mass: 34377.926 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, 493 molecules

#2: 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
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 472 / 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: 2.71 Å3/Da / Density % sol: 54.54 %
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: 1.03317 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 1.9→19.65 Å / Num. obs: 85892 / % possible obs: 99.4 % / Redundancy: 4.17 % / CC1/2: 0.999 / Rrim(I) all: 0.076 / Net I/σ(I): 16.11
Reflection shellResolution: 1.9→2 Å / Mean I/σ(I) obs: 2.49 / Num. unique obs: 12226 / CC1/2: 0.88 / Rrim(I) all: 0.72 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→19.65 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.111 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22346 4352 5 %RANDOM
Rwork0.21333 ---
obs0.21384 82670 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.838 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å2-0 Å2-2.3 Å2
2--3.54 Å20 Å2
3----1.45 Å2
Refinement stepCycle: 1 / Resolution: 1.9→19.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6706 0 95 472 7273
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0127212
X-RAY DIFFRACTIONr_bond_other_d00.0166539
X-RAY DIFFRACTIONr_angle_refined_deg0.7751.8229817
X-RAY DIFFRACTIONr_angle_other_deg0.2881.77115061
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9145870
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.475547
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.094101194
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.040.21013
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.028721
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021755
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_it2.3842.9513416
X-RAY DIFFRACTIONr_mcbond_other2.3822.953413
X-RAY DIFFRACTIONr_mcangle_it3.2575.3084297
X-RAY DIFFRACTIONr_mcangle_other3.2575.3084298
X-RAY DIFFRACTIONr_scbond_it3.2613.3363796
X-RAY DIFFRACTIONr_scbond_other3.2613.3373797
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9275.9665518
X-RAY DIFFRACTIONr_long_range_B_refined6.54835.668087
X-RAY DIFFRACTIONr_long_range_B_other6.54835.668088
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 321 -
Rwork0.359 6081 -
obs--99.61 %

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