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- PDB-6n9q: Structure of the Quorum Quenching lactonase from Parageobacillus ... -

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Basic information

Entry
Database: PDB / ID: 6n9q
TitleStructure of the Quorum Quenching lactonase from Parageobacillus caldoxylosilyticus bind to substrate C4-AHL
ComponentsLactonase GcL
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-[(3S)-2-oxotetrahydrofuran-3-yl]butanamide / TRIETHYLENE GLYCOL / quorum-quenching N-acyl-homoserine lactonase
Similarity search - Component
Biological speciesParageobacillus caldoxylosilyticus NBRC 107762 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _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

Downloads & links

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Assembly

Deposited unit
P: Lactonase GcL
D: Lactonase GcL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,62439
Polymers64,9102
Non-polymers3,71437
Water3,351186
1
D: Lactonase GcL
hetero molecules

P: Lactonase GcL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,62439
Polymers64,9102
Non-polymers3,71437
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
Buried area9020 Å2
ΔGint-36 kcal/mol
Surface area23720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.020, 108.020, 222.140
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 PD

#1: Protein Lactonase GcL


Mass: 32454.850 Da / Num. of mol.: 2
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, 223 molecules

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


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-HL4 / N-[(3S)-2-oxotetrahydrofuran-3-yl]butanamide / N-butyryl-L-homoserine lactone


Mass: 171.194 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H13NO3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#8: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#9: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 3.84 Å3/Da / Density % sol: 67.99 %
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 3-oxo-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-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.35→19.74 Å / Num. obs: 39818 / % possible obs: 98.9 % / Redundancy: 7.35 % / Net I/σ(I): 12.41
Reflection shellResolution: 2.35→2.45 Å

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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: 2.35→19.74 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.594 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.213 / ESU R Free: 0.185 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21093 1991 5 %RANDOM
Rwork0.16623 ---
obs0.16846 37826 98.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 44.767 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 2.35→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4492 0 229 186 4907
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0144961
X-RAY DIFFRACTIONr_bond_other_d00.0174346
X-RAY DIFFRACTIONr_angle_refined_deg0.5671.6916667
X-RAY DIFFRACTIONr_angle_other_deg0.7491.71210216
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5685578
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.31722.903279
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.06915797
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2951528
X-RAY DIFFRACTIONr_chiral_restr0.0280.2608
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025480
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02924
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_it3.6073.9582294
X-RAY DIFFRACTIONr_mcbond_other3.6013.9552292
X-RAY DIFFRACTIONr_mcangle_it4.7055.9372876
X-RAY DIFFRACTIONr_mcangle_other4.7085.9382877
X-RAY DIFFRACTIONr_scbond_it5.5034.7832667
X-RAY DIFFRACTIONr_scbond_other5.4914.7832667
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.7686.8123792
X-RAY DIFFRACTIONr_long_range_B_refined9.84847.3165513
X-RAY DIFFRACTIONr_long_range_B_other9.85147.3245514
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.41 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 144 -
Rwork0.221 2749 -
obs--98.4 %

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