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- PDB-9azy: Crystal structure of PDC-88 beta-lactamase -

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Basic information

Entry
Database: PDB / ID: 9azy
TitleCrystal structure of PDC-88 beta-lactamase
ComponentsBeta-lactamase
KeywordsHYDROLASE / Beta-lactamase / AmpC
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
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKumar, V. / van den Akker, F.
Funding support United States, 1items
OrganizationGrant numberCountry
VenatoRx Pharmaceuticals United States
CitationJournal: Antimicrob.Agents Chemother. / Year: 2025
Title: Structure and mechanism of taniborbactam inhibition of the cefepime-hydrolyzing, partial R2-loop deletion Pseudomonas -derived cephalosporinase variant PDC-88.
Authors: Mack, A.R. / Kumar, V. / Bethel, C.R. / Taracila, M.A. / Miller, B.A. / Uehara, T. / Six, D.A. / Papp-Wallace, K.M. / van den Akker, F. / Bonomo, R.A.
History
DepositionMar 11, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2025Group: 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 / _citation_author.name
Revision 1.2Jul 9, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)40,5961
Polymers40,5961
Non-polymers00
Water8,449469
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.710, 70.019, 106.972
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: 40595.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0K0QVE0, beta-lactamase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 469 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.06 Å3/Da / Density % sol: 40.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100 mM imidazole, pH 7.0, 2-15% isopropyl alcohol, 16-34% PEG3340

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 1.5→29.29 Å / Num. obs: 54555 / % possible obs: 99.6 % / Redundancy: 6.6 % / CC1/2: 1 / Rmerge(I) obs: 0.098 / Net I/σ(I): 9.6
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.638 / Mean I/σ(I) obs: 2 / Num. unique obs: 3777 / CC1/2: 0.9 / % possible all: 94.4

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→29.29 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.708 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2019 2678 4.9 %RANDOM
Rwork0.1672 ---
obs0.1689 51811 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: 90.71 Å2 / Biso mean: 19.822 Å2 / Biso min: 10.16 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.5→29.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2742 0 0 469 3211
Biso mean---32.52 -
Num. residues----353
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132939
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172809
X-RAY DIFFRACTIONr_angle_refined_deg1.6381.6484021
X-RAY DIFFRACTIONr_angle_other_deg1.4821.586465
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8715388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.96221.369168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.79415482
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4261526
X-RAY DIFFRACTIONr_chiral_restr0.080.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023441
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02723
LS refinement shellResolution: 1.5→1.538 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.321 179 -
Rwork0.276 3637 -
obs--95.83 %

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