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- PDB-6n9r: Structure of the Quorum Quenching lactonase from Parageobacillus ... -

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Basic information

Entry
Database: PDB / ID: 6n9r
TitleStructure of the Quorum Quenching lactonase from Parageobacillus caldoxylosilyticus bound to substrate 3-oxo-C12-AHL
ComponentsPutative hydrolase
KeywordsHYDROLASE / lactonase / quorum sensing / thermophile / MLL / quorum quenching / AHL
Function / homology
Function and homology information


quorum-quenching N-acyl-homoserine lactonase / hydrolase activity
Similarity search - Function
Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / : / : / N-3-OXO-DODECANOYL-L-HOMOSERINE LACTONE / TRIETHYLENE GLYCOL / quorum-quenching N-acyl-homoserine lactonase
Similarity search - Component
Biological speciesParageobacillus caldoxylosilyticus NBRC 107762 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsBergonzi, C. / Schwab, M. / Elias, M.
CitationJournal: Chembiochem / Year: 2019
Title: The Structural Determinants Accounting for the Broad Substrate Specificity of the Quorum Quenching Lactonase GcL.
Authors: Bergonzi, C. / Schwab, M. / Naik, T. / Elias, M.
History
DepositionDec 3, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative hydrolase
P: Putative hydrolase
X: Putative hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,26145
Polymers103,1373
Non-polymers4,12442
Water8,125451
1
P: Putative hydrolase
X: Putative hydrolase
hetero molecules

P: Putative hydrolase
X: Putative hydrolase
hetero molecules

A: Putative hydrolase
hetero molecules

A: Putative hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,52290
Polymers206,2736
Non-polymers8,24984
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
crystal symmetry operation3_454x-1/2,y+1/2,z-11
crystal symmetry operation4_555-x+1/2,y+1/2,-z1
Buried area34590 Å2
ΔGint-338 kcal/mol
Surface area62020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.010, 108.590, 78.600
Angle α, β, γ (deg.)90.00, 115.75, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11P-433-

HOH

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Components

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Protein , 1 types, 3 molecules APX

#1: Protein Putative hydrolase /


Mass: 34378.914 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parageobacillus caldoxylosilyticus NBRC 107762 (bacteria)
Gene: GCA01S_030_00190 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A023DFE8

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Non-polymers , 9 types, 493 molecules

#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-OHN / N-3-OXO-DODECANOYL-L-HOMOSERINE LACTONE


Mass: 297.390 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H27NO4
#5: Chemical
ChemComp-ACT / ACETATE ION / Acetate


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


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#9: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 451 / Source method: isolated from a natural source / Formula: H2O

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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: 2.86 Å3/Da / Density % sol: 57.03 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: Concentrated protein samples 10mg.mL-1, ammonium sulfate 1 to 2.25M, 0.1M sodium acetate. Soaking in 20 mM of C12 AHL for 5 min. Diffraction quality crystals appeared after 1 d at 292 K
PH range: 4.0 to 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: Nov 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03333 Å / Relative weight: 1
ReflectionResolution: 1.75→70.8 Å / Num. obs: 109519 / % possible obs: 99.2 % / Redundancy: 3.98 % / CC1/2: 0.999 / Rrim(I) all: 0.059 / Rsym value: 0.051 / Net I/σ(I): 15.21
Reflection shellResolution: 1.75→1.85 Å / Redundancy: 4.07 % / Mean I/σ(I) obs: 3.32 / Num. unique obs: 16825 / CC1/2: 0.947 / Rrim(I) all: 0.48 / Rsym value: 0.419 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6N9I

6n9i


Resolution: 1.75→70.8 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.931 / SU B: 6.959 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.115 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23481 5476 5 %RANDOM
Rwork0.17597 ---
obs0.17894 104043 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.912 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å2-0.05 Å2
2---0.04 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.75→70.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6711 0 250 451 7412
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0147611
X-RAY DIFFRACTIONr_bond_other_d00.0186630
X-RAY DIFFRACTIONr_angle_refined_deg0.5951.68110302
X-RAY DIFFRACTIONr_angle_other_deg0.9871.69115623
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.655918
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.53823.093430
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.905151262
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3881542
X-RAY DIFFRACTIONr_chiral_restr0.030.2941
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.028637
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021437
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_it3.3761.9743572
X-RAY DIFFRACTIONr_mcbond_other3.321.9723568
X-RAY DIFFRACTIONr_mcangle_it3.8862.9764520
X-RAY DIFFRACTIONr_mcangle_other3.8882.9774521
X-RAY DIFFRACTIONr_scbond_it5.0442.5294039
X-RAY DIFFRACTIONr_scbond_other5.0422.5294039
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8363.5975783
X-RAY DIFFRACTIONr_long_range_B_refined5.25724.4268650
X-RAY DIFFRACTIONr_long_range_B_other5.25324.4258650
X-RAY DIFFRACTIONr_rigid_bond_restr10.352314240
X-RAY DIFFRACTIONr_sphericity_free26.5585250
X-RAY DIFFRACTIONr_sphericity_bonded15.976514248
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 403 -
Rwork0.228 7660 -
obs--99.42 %

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