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- PDB-2a7m: 1.6 Angstrom Resolution Structure of the Quorum-Quenching N-Acyl ... -

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Basic information

Entry
Database: PDB / ID: 2a7m
Title1.6 Angstrom Resolution Structure of the Quorum-Quenching N-Acyl Homoserine Lactone Hydrolase of Bacillus thuringiensis
ComponentsN-acyl homoserine lactone hydrolase
KeywordsHYDROLASE / bimetallohydrolase / bimetallo di-zinc / lactonase acyl homoserine / quorum quenching N-acyl / n-acyl
Function / homology
Function and homology information


acyl-L-homoserine-lactone lactonohydrolase activity / quorum-quenching N-acyl-homoserine lactonase / metal ion binding
Similarity search - Function
Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
N-acyl homoserine lactonase AiiA / N-acyl homoserine lactonase
Similarity search - Component
Biological speciesBacillus thuringiensis serovar kurstaki (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsLiu, D. / Lepore, B.W. / Petsko, G.A. / Thomas, P.W. / Stone, E.M. / Fast, W. / Ringe, D.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: Three-dimensional structure of the quorum-quenching N-acyl homoserine lactone hydrolase from Bacillus thuringiensis
Authors: Liu, D. / Lepore, B.W. / Petsko, G.A. / Thomas, P.W. / Stone, E.M. / Fast, W. / Ringe, D.
History
DepositionJul 5, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 14, 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 / struct_site
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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-acyl homoserine lactone hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,11811
Polymers28,2501
Non-polymers86810
Water3,261181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.600, 55.551, 80.094
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsbiologically relevant entity is monomeric, and is contained by the entire asymmetric unit, and no symmetry operators are required.

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Components

#1: Protein N-acyl homoserine lactone hydrolase


Mass: 28250.162 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis serovar kurstaki (bacteria)
Species: Bacillus thuringiensis / Strain: serovar kurstaki / Gene: aiia / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha
References: UniProt: Q7B8C3, UniProt: P0CJ63*PLUS, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.19 Å3/Da / Density % sol: 43.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: glycerol, tris-hcl, peg4000, magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL11-110.8265
SYNCHROTRONAPS 14-BM-D21.2827
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDApr 25, 2005
ADSC QUANTUM 42CCDFeb 21, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Curved CrystalSINGLE WAVELENGTHMx-ray1
2Si 111SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.82651
21.28271
ReflectionResolution: 1.6→50 Å / Num. obs: 32757 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 36.8
Reflection shellResolution: 1.6→1.686 Å / Redundancy: 7 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 2.4 / Num. unique all: 3603 / Rsym value: 0.87 / % possible all: 80.49

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
Blu-Icedata collection
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→45.64 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.105 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.099 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Atoms with little to no electron density are represented in this PDB file as having zero occupancy, and the atomic displacement parameters for these atoms have been set to zero. These atoms ...Details: Atoms with little to no electron density are represented in this PDB file as having zero occupancy, and the atomic displacement parameters for these atoms have been set to zero. These atoms have been included in this file with geometry corresponding to that which would be obtained in refinement, however they were not included in the calculations for the residuals. Residues ASP A 50 and ILE A 190 exist in generously allowed and disallowed sectors of the Ramachandran plot and exhibit outstanding omit map electron density. ILE A 142 is on the edge of the additionally allowed and generously allowed sector of the plot as calculated with PROCHECK and MOLEMAN2.
RfactorNum. reflection% reflectionSelection details
Rfree0.21068 1420 4.7 %RANDOM
Rwork0.16976 ---
all0.17171 28550 --
obs0.17171 28550 91.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.651 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å20 Å20 Å2
2---0.96 Å20 Å2
3---0.11 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.29 Å
Luzzati d res low-1.6 Å
Luzzati sigma a0.17 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.6→45.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1989 0 50 181 2220
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222173
X-RAY DIFFRACTIONr_angle_refined_deg1.3052.0112931
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1895250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.40925.36895
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.29415397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.213156
X-RAY DIFFRACTIONr_chiral_restr0.0850.2339
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021555
X-RAY DIFFRACTIONr_nbd_refined0.2010.21074
X-RAY DIFFRACTIONr_nbtor_refined0.310.21481
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1140.2169
X-RAY DIFFRACTIONr_metal_ion_refined0.0330.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1020.217
X-RAY DIFFRACTIONr_mcbond_it1.73421317
X-RAY DIFFRACTIONr_mcangle_it2.2932098
X-RAY DIFFRACTIONr_scbond_it3.7124957
X-RAY DIFFRACTIONr_scangle_it5.1736833
LS refinement shellResolution: 1.6→1.686 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.299 192 -
Rwork0.234 3603 -
obs--80.49 %
Refinement TLS params.Method: refined / Origin x: 19.919 Å / Origin y: 30.759 Å / Origin z: 29.698 Å
111213212223313233
T-0.0668 Å20.0156 Å20.0107 Å2--0.0607 Å2-0.0141 Å2---0.0895 Å2
L1.8182 °2-0.5265 °20.241 °2-2.2137 °20.1824 °2--0.9932 °2
S-0.0854 Å °-0.2562 Å °0.0257 Å °0.1552 Å °0.0478 Å °0.148 Å °0.0047 Å °-0.1194 Å °0.0375 Å °

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