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- PDB-9b2l: Structure of the quorum quenching lactonase GcL D122N mutant - bi... -

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Basic information

Entry
Database: PDB / ID: 9b2l
TitleStructure of the quorum quenching lactonase GcL D122N mutant - bimetallic 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
: / : / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Putative hydrolase
Similarity search - Component
Biological speciesParageobacillus caldoxylosilyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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
A: quorum-quenching N-acyl-homoserine lactonase
B: quorum-quenching N-acyl-homoserine lactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,55015
Polymers63,4502
Non-polymers1,10013
Water1,982110
1
A: quorum-quenching N-acyl-homoserine lactonase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)64,55015
Polymers63,4502
Non-polymers1,10013
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area4410 Å2
ΔGint-106 kcal/mol
Surface area22830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.220, 109.220, 221.660
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 AB

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


Mass: 31724.941 Da / Num. of mol.: 2 / Mutation: D122N
Source method: isolated from a genetically manipulated source
Details: D122N mutation
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 , 7 types, 123 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 3.97 Å3/Da / Density % sol: 68.98 %
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 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03333 Å / Relative weight: 1
ReflectionResolution: 2.2→73.89 Å / Num. obs: 49981 / % possible obs: 99.8 % / Redundancy: 6.21 % / CC1/2: 0.998 / Net I/σ(I): 10.58
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 6.34 % / Num. unique obs: 6245 / CC1/2: 0.918 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→73.89 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.943 / SU B: 6.838 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24148 2498 5 %RANDOM
Rwork0.21407 ---
obs0.21546 47460 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.575 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20.14 Å20 Å2
2--0.27 Å2-0 Å2
3----0.88 Å2
Refinement stepCycle: 1 / Resolution: 2.2→73.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4516 0 4 110 4630
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0124679
X-RAY DIFFRACTIONr_bond_other_d00.0164261
X-RAY DIFFRACTIONr_angle_refined_deg0.7641.6676345
X-RAY DIFFRACTIONr_angle_other_deg0.2581.5879811
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6335556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.383528
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.30610767
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0380.2654
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025586
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021126
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_it4.5965.3732218
X-RAY DIFFRACTIONr_mcbond_other4.5945.3742218
X-RAY DIFFRACTIONr_mcangle_it5.919.672776
X-RAY DIFFRACTIONr_mcangle_other5.919.6692777
X-RAY DIFFRACTIONr_scbond_it6.4676.1312461
X-RAY DIFFRACTIONr_scbond_other6.4666.1322462
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.18910.8933570
X-RAY DIFFRACTIONr_long_range_B_refined10.45157.75093
X-RAY DIFFRACTIONr_long_range_B_other10.45357.765073
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.579 186 -
Rwork0.559 3551 -
obs--99.97 %

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