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- PDB-6cgz: Structure of the Quorum Quenching lactonase from Alicyclobacillus... -

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Basic information

Entry
Database: PDB / ID: 6cgz
TitleStructure of the Quorum Quenching lactonase from Alicyclobacillus acidoterrestris bound to C6-AHL
ComponentsBeta-lactamase
KeywordsHYDROLASE / lactonase / acyl homoserine lactone hydrolase
Function / homology
Function and homology information


: / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / N-[(3S)-2-oxotetrahydrofuran-3-yl]hexanamide / N-acyl homoserine lactonase family protein
Similarity search - Component
Biological speciesAlicyclobacillus acidoterrestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsBergonzi, C. / Schwab, M. / Naik, T. / Daude, D. / Chabriere, E. / Elias, M.
Funding support United States, 1items
OrganizationGrant numberCountry
MnDrive United States
Citation
Journal: Sci Rep / Year: 2018
Title: Structural and Biochemical Characterization of AaL, a Quorum Quenching Lactonase with Unusual Kinetic Properties.
Authors: Bergonzi, C. / Schwab, M. / Naik, T. / Daude, D. / Chabriere, E. / Elias, M.
#1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: The quorum-quenching lactonase from Alicyclobacter acidoterrestris: purification, kinetic characterization, crystallization and crystallographic analysis.
Authors: Bergonzi, C. / Schwab, M. / Chabriere, E. / Elias, M.
History
DepositionFeb 21, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,45823
Polymers96,2353
Non-polymers2,22320
Water10,701594
1
A: Beta-lactamase
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,77617
Polymers64,1572
Non-polymers1,61915
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-14 kcal/mol
Surface area22970 Å2
MethodPISA
2
C: Beta-lactamase
hetero molecules

C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,36412
Polymers64,1572
Non-polymers1,20710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area3120 Å2
ΔGint-19 kcal/mol
Surface area24210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.940, 88.690, 97.680
Angle α, β, γ (deg.)90.00, 128.24, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-403-

HOH

21C-470-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Beta-lactamase


Mass: 32078.346 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alicyclobacillus acidoterrestris (strain ATCC 49025 / DSM 3922 / CIP 106132 / NCIMB 13137 / GD3B) (bacteria)
Strain: ATCC 49025 / DSM 3922 / CIP 106132 / NCIMB 13137 / GD3B
Gene: N007_09425 / Production host: Escherichia coli (E. coli) / References: UniProt: T0BMH6

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Non-polymers , 6 types, 614 molecules

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


Mass: 58.933 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Co
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-HL6 / N-[(3S)-2-oxotetrahydrofuran-3-yl]hexanamide / N-hexanoyl-L-homoserine lactone


Mass: 199.247 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H17NO3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 594 / 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: 2.58 Å3/Da / Density % sol: 52.32 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Purified and concentrated AaL samples (10 mg ml) were subjected to crystallization trialsCrystals appeared after 1 d at 292 K in a condition consisting of 0.45M ammonium chloride, 16% ...Details: Purified and concentrated AaL samples (10 mg ml) were subjected to crystallization trialsCrystals appeared after 1 d at 292 K in a condition consisting of 0.45M ammonium chloride, 16% polyethylene glycol 3350. Seeding was performed as described previously (PMID: 28777091)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03312 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03312 Å / Relative weight: 1
ReflectionResolution: 1.8→57.31 Å / Num. obs: 90111 / % possible obs: 99.2 % / Redundancy: 4.2 % / Rsym value: 0.054 / Net I/σ(I): 18.27
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.3 % / Num. unique obs: 13463 / Rsym value: 0.59 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementResolution: 1.8→57.31 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.528 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.105 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19241 4506 5 %RANDOM
Rwork0.16345 ---
obs0.1649 85605 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.114 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.8→57.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6621 0 132 594 7347
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0197196
X-RAY DIFFRACTIONr_bond_other_d0.0020.026669
X-RAY DIFFRACTIONr_angle_refined_deg1.3431.949737
X-RAY DIFFRACTIONr_angle_other_deg0.7773.00315413
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9365872
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.99524.417360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.583151192
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3141540
X-RAY DIFFRACTIONr_chiral_restr0.080.2995
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218209
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021707
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_it1.5252.5433443
X-RAY DIFFRACTIONr_mcbond_other1.5252.5433444
X-RAY DIFFRACTIONr_mcangle_it2.2363.8034330
X-RAY DIFFRACTIONr_mcangle_other2.2363.8034331
X-RAY DIFFRACTIONr_scbond_it2.2232.9073753
X-RAY DIFFRACTIONr_scbond_other2.2222.9073753
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5784.2255408
X-RAY DIFFRACTIONr_long_range_B_refined5.28421.4088684
X-RAY DIFFRACTIONr_long_range_B_other5.28421.4078684
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 332 -
Rwork0.284 6307 -
obs--99.64 %

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