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- PDB-6n9i: Structure of the Quorum Quenching lactonase from Parageobacillus ... -

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Basic information

Entry
Database: PDB / ID: 6n9i
TitleStructure of the Quorum Quenching lactonase from Parageobacillus caldoxylosilyticus - free
ComponentsPutative hydrolase
KeywordsHYDROLASE / lactonase / quorum sensing / thermophile / MLL / quorum quenching / AHL
Function / homology
Function and homology information


hydrolase activity / metal ion binding
Similarity search - Function
: / 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
ACETATE ION / : / : / TRIETHYLENE GLYCOL / Putative hydrolase
Similarity search - Component
Biological speciesParageobacillus caldoxylosilyticus NBRC 107762 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 1.1May 1, 2019Group: Data collection / Derived calculations / Category: struct_conn / struct_conn_type
Revision 1.2Aug 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 1.3Oct 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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: Putative hydrolase
B: Putative hydrolase
C: Putative hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,85651
Polymers103,1373
Non-polymers3,71948
Water11,836657
1
A: Putative hydrolase
hetero molecules

C: Putative hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,95731
Polymers68,7582
Non-polymers2,19929
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556-x+1/2,y+1/2,-z+11
Buried area7490 Å2
ΔGint-102 kcal/mol
Surface area23050 Å2
MethodPISA
2
B: Putative hydrolase
hetero molecules

B: Putative hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,79840
Polymers68,7582
Non-polymers3,04038
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area8650 Å2
ΔGint-184 kcal/mol
Surface area24460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.420, 108.680, 78.740
Angle α, β, γ (deg.)90.00, 115.84, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-519-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

#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 , 8 types, 705 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-ACT / ACETATE ION


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


Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe
#7: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 657 / 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: 2.88 Å3/Da / Density % sol: 57.23 %
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. 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: 1.03323 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03323 Å / Relative weight: 1
ReflectionResolution: 1.6→63.93 Å / Num. obs: 602221 / % possible obs: 99.6 % / Redundancy: 4.17 % / CC1/2: 0.1 / Rrim(I) all: 0.033 / Net I/σ(I): 26.5
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 4.15 % / Mean I/σ(I) obs: 3.1 / Num. unique obs: 23974 / CC1/2: 0.994 / Rrim(I) all: 0.645 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2r2d

2r2d


Resolution: 1.6→63.93 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.964 / SU B: 4.1 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.074 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1873 7222 5 %RANDOM
Rwork0.1394 ---
obs0.14178 137203 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.224 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20.22 Å2
2---0.26 Å2-0 Å2
3---0.04 Å2
Refinement stepCycle: 1 / Resolution: 1.6→63.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6711 0 213 657 7581
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0147572
X-RAY DIFFRACTIONr_bond_other_d00.0176529
X-RAY DIFFRACTIONr_angle_refined_deg0.6961.67710272
X-RAY DIFFRACTIONr_angle_other_deg0.8981.66815376
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7595924
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.84422.779439
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.893151261
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8921547
X-RAY DIFFRACTIONr_chiral_restr0.0370.2942
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028658
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021438
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_it4.6942.8613561
X-RAY DIFFRACTIONr_mcbond_other4.6572.8563553
X-RAY DIFFRACTIONr_mcangle_it5.1734.3134517
X-RAY DIFFRACTIONr_mcangle_other5.1734.3134518
X-RAY DIFFRACTIONr_scbond_it6.9213.4324011
X-RAY DIFFRACTIONr_scbond_other6.923.4324011
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.5724.9275753
X-RAY DIFFRACTIONr_long_range_B_refined6.84835.2628861
X-RAY DIFFRACTIONr_long_range_B_other6.84835.2638862
X-RAY DIFFRACTIONr_rigid_bond_restr7.741314100
X-RAY DIFFRACTIONr_sphericity_free27.5425337
X-RAY DIFFRACTIONr_sphericity_bonded21.389514230
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 534 -
Rwork0.256 10137 -
obs--99.76 %

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