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- PDB-7y7u: Dimeric structure of a Quorum-Quenching metallo-hydrolase, LrsL -

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Basic information

Entry
Database: PDB / ID: 7y7u
TitleDimeric structure of a Quorum-Quenching metallo-hydrolase, LrsL
ComponentsMBL fold metallo-hydrolase
KeywordsHYDROLASE / Quorum-quenching / lactonase / metallo-hydrolase / Labrenzia sp.
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 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
MBL fold metallo-hydrolase
Similarity search - Component
Biological speciesLabrenzia sp. VG12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsMomin, A.A. / Arold, S.T.
Funding support Saudi Arabia, 1items
OrganizationGrant numberCountry
Other privateBAS/1/1056-01-01 Saudi Arabia
CitationJournal: Front Microbiol / Year: 2022
Title: The exceptionally efficient quorum quenching enzyme LrsL suppresses Pseudomonas aeruginosa biofilm production.
Authors: Rehman, Z.U. / Momin, A.A. / Aldehaiman, A. / Irum, T. / Grunberg, R. / Arold, S.T.
History
DepositionJun 22, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2022Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MBL fold metallo-hydrolase
B: MBL fold metallo-hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8896
Polymers63,6272
Non-polymers2624
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, Protein elutes as a dimer in size exclusion, and dimeric molecular weight confirmed by Multi-angle light scattering (SEC-MALS)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-175 kcal/mol
Surface area22730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.510, 166.510, 166.510
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132

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Components

#1: Protein MBL fold metallo-hydrolase / Quorum-Quenching metallo-hydrolase / LrsL


Mass: 31813.711 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: GB ASP32504.1 / Source: (gene. exp.) Labrenzia sp. VG12 (bacteria) / Gene: CHH27_03985 / Plasmid: pJEx411c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A222F232
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.02 Å3/Da / Density % sol: 59.31 % / Description: Cubic
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 1.6 M tri-Sodium citrate tribasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 27, 2022
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.89→46.18 Å / Num. obs: 63574 / % possible obs: 99.97 % / Redundancy: 81.3 % / Biso Wilson estimate: 44.72 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.1542 / Rpim(I) all: 0.01717 / Rrim(I) all: 0.1552 / Net I/σ(I): 31.63
Reflection shellResolution: 1.89→1.958 Å / Redundancy: 83.6 % / Rmerge(I) obs: 6.561 / Mean I/σ(I) obs: 0.71 / Num. unique obs: 6220 / CC1/2: 0.368 / CC star: 0.734 / Rpim(I) all: 0.7185 / Rrim(I) all: 6.601 / % possible all: 99.98

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Processing

Software
NameVersionClassification
REFMAC5.8.0349refinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P9E

1p9e


Resolution: 1.89→46.18 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.881 / SU ML: 0.107 / Cross valid method: FREE R-VALUE / ESU R: 0.121 / ESU R Free: 0.124 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2349 2000 3.146 %
Rwork0.1908 61574 -
all0.192 --
obs-63574 99.881 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 47.577 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.89→46.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4386 0 4 293 4683
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0124543
X-RAY DIFFRACTIONr_angle_refined_deg1.7191.6396180
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4045580
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.3491028
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.19810675
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.0110215
X-RAY DIFFRACTIONr_chiral_restr0.110.2661
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023550
X-RAY DIFFRACTIONr_nbd_refined0.2110.21951
X-RAY DIFFRACTIONr_nbtor_refined0.3130.23051
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2333
X-RAY DIFFRACTIONr_metal_ion_refined0.0480.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1980.244
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1370.211
X-RAY DIFFRACTIONr_mcbond_it4.2084.4982317
X-RAY DIFFRACTIONr_mcangle_it5.5366.7142898
X-RAY DIFFRACTIONr_scbond_it5.8164.8842226
X-RAY DIFFRACTIONr_scangle_it8.0447.1193282
X-RAY DIFFRACTIONr_lrange_it10.41889.17819480
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.9360.4811440.4744419X-RAY DIFFRACTION98.5316
1.936-1.9890.371410.3714375X-RAY DIFFRACTION100
1.989-2.0470.3311380.3094229X-RAY DIFFRACTION100
2.047-2.1090.2941330.2574114X-RAY DIFFRACTION100
2.109-2.1780.2861310.2354016X-RAY DIFFRACTION100
2.178-2.2550.271270.2233877X-RAY DIFFRACTION100
2.255-2.340.2751210.2223770X-RAY DIFFRACTION100
2.34-2.4350.2521170.2073595X-RAY DIFFRACTION100
2.435-2.5430.2371140.23490X-RAY DIFFRACTION100
2.543-2.6670.2591080.2063325X-RAY DIFFRACTION100
2.667-2.810.251020.2143166X-RAY DIFFRACTION100
2.81-2.980.292990.2213047X-RAY DIFFRACTION100
2.98-3.1850.268920.2112831X-RAY DIFFRACTION100
3.185-3.4390.222860.1852656X-RAY DIFFRACTION100
3.439-3.7650.247810.1682459X-RAY DIFFRACTION100
3.765-4.2070.221730.1552251X-RAY DIFFRACTION100
4.207-4.8510.144650.1222002X-RAY DIFFRACTION100
4.851-5.9260.182550.151723X-RAY DIFFRACTION100
5.926-8.3180.191460.181379X-RAY DIFFRACTION100
8.318-46.180.241270.201850X-RAY DIFFRACTION100

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