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- PDB-8sdv: Crystal structure of PDC-3 Y221H beta-lactamase in complex with t... -

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Basic information

Entry
Database: PDB / ID: 8sdv
TitleCrystal structure of PDC-3 Y221H beta-lactamase in complex with the boronic acid inhibitor S02030
ComponentsBeta-lactamase
KeywordsHYDROLASE / Pseudomonas-derived Cephalosporinase / antibiotic 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/transpeptidase-like
Similarity search - Domain/homology
IMIDAZOLE / Chem-ZXM / Beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsKumar, V. / van den Akker, F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI063517 United States
CitationJournal: Antimicrob.Agents Chemother. / Year: 2023
Title: Natural protein engineering in the Omega-loop: the role of Y221 in ceftazidime and ceftolozane resistance in Pseudomonas -derived cephalosporinase.
Authors: Mack, A.R. / Kumar, V. / Taracila, M.A. / Mojica, M.F. / O'Shea, M. / Schinabeck, W. / Silver, G. / Hujer, A.M. / Papp-Wallace, K.M. / Chen, S. / Haider, S. / Caselli, E. / Prati, F. / van ...Authors: Mack, A.R. / Kumar, V. / Taracila, M.A. / Mojica, M.F. / O'Shea, M. / Schinabeck, W. / Silver, G. / Hujer, A.M. / Papp-Wallace, K.M. / Chen, S. / Haider, S. / Caselli, E. / Prati, F. / van den Akker, F. / Bonomo, R.A.
History
DepositionApr 7, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)44,0917
Polymers43,3941
Non-polymers6976
Water8,863492
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)44.685, 71.765, 104.784
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: 43394.168 Da / Num. of mol.: 1 / Mutation: Y221H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: ampC / Production host: Escherichia coli (E. coli) / References: UniProt: Q4H482, beta-lactamase
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical ChemComp-ZXM / 1-{(2R)-2-(dihydroxyboranyl)-2-[(thiophen-2-ylacetyl)amino]ethyl}-1H-1,2,3-triazole-4-carboxylic acid


Mass: 324.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13BN4O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 492 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 1.94 Å3/Da / Density % sol: 36.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100 mM Imidazole pH 7.0, 2-8% isopropyl alcohol (IPA), and 16-34% PEG 3350. The protein is in 10 mM HEPES pH 7.5, 150 mM NaCl and 5% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97935 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.42→29.62 Å / Num. obs: 64139 / % possible obs: 99.6 % / Redundancy: 13.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Net I/σ(I): 20.6
Reflection shellResolution: 1.42→1.46 Å / Redundancy: 12 % / Rmerge(I) obs: 0.704 / Mean I/σ(I) obs: 3 / Num. unique obs: 4477 / CC1/2: 0.883 / % possible all: 95.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3S22

3s22


Resolution: 1.42→29.62 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.91 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1642 3163 4.9 %RANDOM
Rwork0.1466 ---
obs0.1475 60901 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85.67 Å2 / Biso mean: 15.346 Å2 / Biso min: 8.03 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.42→29.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2778 0 49 492 3319
Biso mean--20.57 27.79 -
Num. residues----360
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133072
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172932
X-RAY DIFFRACTIONr_angle_refined_deg1.651.6524208
X-RAY DIFFRACTIONr_angle_other_deg1.4651.5776749
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.725403
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.8721.092174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.79815489
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4771528
X-RAY DIFFRACTIONr_chiral_restr0.0860.2378
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023630
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02758
LS refinement shellResolution: 1.421→1.458 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 198 -
Rwork0.204 4273 -
all-4471 -
obs--95.17 %

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