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- PDB-9q0a: CTX-M-14 WT in complex with BLIP E73W -

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Basic information

Entry
Database: PDB / ID: 9q0a
TitleCTX-M-14 WT in complex with BLIP E73W
Components
  • Beta-lactamase
  • Beta-lactamase inhibitory protein
KeywordsHYDROLASE/PROTEIN BINDING / Antibiotic resistance / inhibition / BLIP / beta-lactamase / PROTEIN BINDING / HYDROLASE-PROTEIN BINDING complex
Function / homology
Function and homology information


regulation of beta-lactamase activity / beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / extracellular region
Similarity search - Function
Beta-lactamase-inhibitor protein BLIP / Beta-lactamase-inhibitor protein BLIP domain superfamily / Beta-lactamase inhibitor (BLIP) / BamE-like / Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Beta-lactamase / Beta-lactamase inhibitory protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Streptomyces clavuligerus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsRivera, P. / Lu, S. / Sankaran, B. / Prasad, B.V.V. / Palzkill, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: J.Biol.Chem. / Year: 2025
Title: A beta-lactamase inhibitory protein mutant displays high potency and a broad inhibition profile due to an altered binding mode with beta-lactamases.
Authors: Rivera, P. / Lu, S. / Ngango, D. / Sankaran, B. / Venkataram Prasad, B.V. / Palzkill, T.
History
DepositionAug 12, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 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
B: Beta-lactamase inhibitory protein


Theoretical massNumber of molelcules
Total (without water)45,6142
Polymers45,6142
Non-polymers00
Water7,080393
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-8 kcal/mol
Surface area16560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.170, 79.890, 118.080
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11B-355-

HOH

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Components

#1: Protein Beta-lactamase


Mass: 28000.547 Da / Num. of mol.: 1 / Fragment: UNP residues 22-284
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CTX-M-14 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H6UQI0, beta-lactamase
#2: Protein Beta-lactamase inhibitory protein / BLIP


Mass: 17613.588 Da / Num. of mol.: 1 / Mutation: E73W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces clavuligerus (bacteria) / Production host: Komagataella pastoris (fungus) / References: UniProt: P35804
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 393 / Source method: isolated from a natural source / Formula: H2O
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: 2.23 Å3/Da / Density % sol: 44.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2 M calcium chloride, 0.1 M sodium acetate pH 5, 20% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.65→47.48 Å / Num. obs: 49766 / % possible obs: 99.45 % / Redundancy: 4.2 % / Biso Wilson estimate: 14.05 Å2 / CC1/2: 0.992 / CC star: 0.998 / Net I/σ(I): 12.28
Reflection shellResolution: 1.65→1.68 Å / Num. unique obs: 2744 / CC1/2: 0.951 / CC star: 0.987

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→47.48 Å / SU ML: 0.1514 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.755
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2115 2518 5.06 %
Rwork0.1861 47248 -
obs0.1874 49766 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.97 Å2
Refinement stepCycle: LAST / Resolution: 1.65→47.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3204 0 0 393 3597
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00573264
X-RAY DIFFRACTIONf_angle_d0.84244441
X-RAY DIFFRACTIONf_chiral_restr0.0501511
X-RAY DIFFRACTIONf_plane_restr0.0086579
X-RAY DIFFRACTIONf_dihedral_angle_d13.55781159
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.680.23081500.19932594X-RAY DIFFRACTION99.75
1.68-1.720.23031360.19232581X-RAY DIFFRACTION99.56
1.72-1.750.23361340.17932577X-RAY DIFFRACTION99.41
1.75-1.790.21711420.16652603X-RAY DIFFRACTION99.67
1.79-1.840.21931170.1792588X-RAY DIFFRACTION99.63
1.84-1.890.21381440.1942603X-RAY DIFFRACTION99.64
1.89-1.940.24741520.21122543X-RAY DIFFRACTION98.54
1.94-2.010.19861520.17622604X-RAY DIFFRACTION99.57
2.01-2.080.20511410.18562585X-RAY DIFFRACTION99.09
2.08-2.160.21721390.17242652X-RAY DIFFRACTION99.71
2.16-2.260.2271340.18852586X-RAY DIFFRACTION99.2
2.26-2.380.2131170.18372636X-RAY DIFFRACTION99.67
2.38-2.530.21161510.19632624X-RAY DIFFRACTION99.75
2.53-2.720.22861370.20552644X-RAY DIFFRACTION99.53
2.72-30.22251280.19992642X-RAY DIFFRACTION99.71
3-3.430.19771540.18752660X-RAY DIFFRACTION99.65
3.43-4.320.20011390.16292718X-RAY DIFFRACTION99.3
4.32-47.480.19131510.18982808X-RAY DIFFRACTION98.83

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