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- PDB-6uqt: Serendipitous Discovery of Aryl Boronic Acids as beta-Lactamase I... -

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Basic information

Entry
Database: PDB / ID: 6uqt
TitleSerendipitous Discovery of Aryl Boronic Acids as beta-Lactamase Inhibitors
ComponentsBeta-lactamase
KeywordsANTIBIOTIC / boronic acid inhibitors / drug resistance
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic
Similarity search - Function
Beta-lactamase, class-C active site / Beta-lactamase class-C active site. / : / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-hydroxyethyl hydrogen (3-methoxyphenyl)boronate / Beta-lactamase / Beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.25 Å
AuthorsScapin, G.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2020
Title: Serendipitous discovery of aryl boronic acids as beta-lactamase inhibitors.
Authors: Yang, S.W. / Pan, J. / Root, Y. / Scapin, G. / Xiao, L. / Su, J.
History
DepositionOct 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 15, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2563
Polymers41,0241
Non-polymers2312
Water9,746541
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.773, 71.398, 105.073
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-lactamase


Mass: 41024.316 Da / Num. of mol.: 1 / Mutation: R397A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: ampC, RW109_RW109_01564 / Production host: Escherichia coli (E. coli)
References: UniProt: Q541D8, UniProt: P24735*PLUS, beta-lactamase
#2: Chemical ChemComp-QFS / 2-hydroxyethyl hydrogen (3-methoxyphenyl)boronate


Mass: 196.008 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13BO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 541 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.05 Å3/Da / Density % sol: 39.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 18% PEG 3350, 10% isopropanol, 100 mM Imidazole, pH=6.5; seeding

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→105.073 Å / Num. all: 93863 / Num. obs: 93863 / % possible obs: 100 % / Redundancy: 6.4 % / Rpim(I) all: 0.017 / Rrim(I) all: 0.043 / Rsym value: 0.036 / Net I/av σ(I): 15 / Net I/σ(I): 25.2 / Num. measured all: 600997
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.25-1.326.40.5191.586217135570.2380.6090.5193.6100
1.32-1.46.30.3762.181550128500.1730.4410.3764.9100
1.4-1.496.30.2293.475826120610.1070.2710.2297.6100
1.49-1.616.60.1395.674561112560.0630.1630.13912.4100
1.61-1.776.40.0839.366469103920.0390.0990.08319.1100
1.77-1.986.60.04915.46210194360.0220.0580.04931100
1.98-2.286.50.03222.65486583790.0150.0370.03247.599.9
2.28-2.86.20.02329.14431271240.0110.0280.02359.799.9
2.8-3.956.40.017353579655710.0080.020.01777.999.9
3.95-105.07360.01536.31930032370.0070.0180.01585.799.7

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALA3.3.20data scaling
REFMAC5.8.0123refinement
PDB_EXTRACT3.25data extraction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.25→59.05 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.971 / SU B: 0.669 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.043 / ESU R Free: 0.043
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1731 4703 5 %RANDOM
Rwork0.1603 ---
obs0.161 89069 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 100.21 Å2 / Biso mean: 15.898 Å2 / Biso min: 6.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å2-0 Å2
2--0.52 Å20 Å2
3---0.14 Å2
Refinement stepCycle: final / Resolution: 1.25→59.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2786 0 15 550 3351
Biso mean--13.33 34.54 -
Num. residues----363
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192938
X-RAY DIFFRACTIONr_bond_other_d0.0020.022785
X-RAY DIFFRACTIONr_angle_refined_deg1.5281.984005
X-RAY DIFFRACTIONr_angle_other_deg0.91936403
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2155380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.08123.582134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.04615465
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.1541523
X-RAY DIFFRACTIONr_chiral_restr0.0890.2430
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213395
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02684
LS refinement shellResolution: 1.25→1.283 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 342 -
Rwork0.234 6507 -
all-6849 -
obs--99.88 %

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