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

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Basic information

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


: / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / PHOSPHATE ION / N-acyl homoserine lactonase family protein
Similarity search - Component
Biological speciesAlicyclobacillus acidoterrestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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 1.1Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
H: Beta-lactamase
L: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,30618
Polymers96,2353
Non-polymers1,07115
Water7,458414
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.720, 114.740, 79.970
Angle α, β, γ (deg.)90.00, 109.78, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-415-

HOH

21H-468-

HOH

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Components

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Protein , 1 types, 3 molecules AHL

#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 , 5 types, 429 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-CO / COBALT (II) ION


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


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / 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: 2.51 Å3/Da / Density % sol: 50.92 %
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-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.65→19.9 Å / Num. obs: 111796 / % possible obs: 98.2 % / Redundancy: 3.86 % / Rsym value: 0.036 / Net I/σ(I): 22.08
Reflection shellResolution: 1.65→1.75 Å / Redundancy: 3.94 % / Mean I/σ(I) obs: 3.16 / Num. unique obs: 17858 / Rsym value: 0.591 / % possible all: 97.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→19.9 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.914 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19737 5590 5 %RANDOM
Rwork0.17039 ---
obs0.17172 106205 98.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0 Å2-0.06 Å2
2--0.01 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.65→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6631 0 49 414 7094
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0197085
X-RAY DIFFRACTIONr_bond_other_d0.0010.026520
X-RAY DIFFRACTIONr_angle_refined_deg1.1641.9339620
X-RAY DIFFRACTIONr_angle_other_deg0.644315054
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3235870
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.69424.494356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.271151184
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8541538
X-RAY DIFFRACTIONr_chiral_restr0.0730.2991
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218152
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021694
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_it2.7222.4973426
X-RAY DIFFRACTIONr_mcbond_other2.7132.4973425
X-RAY DIFFRACTIONr_mcangle_it3.4963.7364314
X-RAY DIFFRACTIONr_mcangle_other3.4983.7364315
X-RAY DIFFRACTIONr_scbond_it4.3392.9193659
X-RAY DIFFRACTIONr_scbond_other4.162.9193647
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0054.2085289
X-RAY DIFFRACTIONr_long_range_B_refined6.76520.678239
X-RAY DIFFRACTIONr_long_range_B_other6.76420.6748240
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 404 -
Rwork0.272 7683 -
obs--97.07 %

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