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- PDB-9azw: Crystal structure of PDC-88 beta-lactamase in complex with tanibo... -

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Basic information

Entry
Database: PDB / ID: 9azw
TitleCrystal structure of PDC-88 beta-lactamase in complex with taniborbactam
ComponentsBeta-lactamase
KeywordsHYDROLASE/ANTIBIOTIC / Beta-lactamase / boronic acid inhibitor. / HYDROLASE-ANTIBIOTIC complex
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / beta-lactamase activity / 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
Chem-KJK / Beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsKumar, V. / van den Akker, F.
Funding support United States, 1items
OrganizationGrant numberCountry
VenatoRx Pharmaceuticals United States
CitationJournal: To Be Published
Title: Mechanisms of Antibiotic Resistance and Inhibition of PDC-88, a Cefepime-Hydrolyzing R2-loop Deletion Variant of Pseudomonas-derived Cephalosporinase
Authors: Mack, A.R. / Kumar, V. / Bethel, C.R. / Taracila, M.A. / Miller, B.A. / Six, D.A. / Uehara, T. / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9852
Polymers40,5961
Non-polymers3891
Water5,188288
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.638, 70.191, 105.893
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: Chemical ChemComp-KJK / (3~{R})-3-[2-[4-(2-azanylethylamino)cyclohexyl]ethanoylamino]-2-oxidanyl-3,4-dihydro-1,2-benzoxaborinine-8-carboxylic acid


Mass: 389.254 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H28BN3O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.04 Å3/Da / Density % sol: 39.8 %
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, crystals soaked with 5-10 mM taniborbactam

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.55→37.69 Å / Num. obs: 48946 / % possible obs: 99.2 % / Redundancy: 11.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.041 / Rrim(I) all: 0.143 / Net I/σ(I): 8.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.55-1.5782.51690421110.5430.9082.6690.888.8
8.48-37.6711.90.07143983690.9970.0210.07427.299.3

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.7data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→37.69 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.966 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2394 2441 5 %RANDOM
Rwork0.202 ---
obs0.2038 46271 98.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 104.11 Å2 / Biso mean: 25.556 Å2 / Biso min: 14.18 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0 Å20 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.55→37.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2760 0 28 288 3076
Biso mean--32.17 35.86 -
Num. residues----356
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132859
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172700
X-RAY DIFFRACTIONr_angle_refined_deg1.6011.6493885
X-RAY DIFFRACTIONr_angle_other_deg1.4251.5816195
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9895355
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.19421.21157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.73115444
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2231524
X-RAY DIFFRACTIONr_chiral_restr0.0850.2352
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023292
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02688
LS refinement shellResolution: 1.55→1.588 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.472 161 -
Rwork0.457 2989 -
obs--87.92 %

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