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- PDB-9q0c: TEM-1 WT in complex with BLIP E73W -

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Basic information

Entry
Database: PDB / ID: 9q0c
TitleTEM-1 WT in complex with BLIP E73W
Components
  • Beta-lactamase TEM
  • Beta-lactamase inhibitory protein
KeywordsHYDROLASE/PROTEIN BINDING / beta-lactamase / inhibitory / protein / BLIP / TEM / 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 inhibitory protein / Beta-lactamase TEM
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Streptomyces clavuligerus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 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 TEM
B: Beta-lactamase inhibitory protein
C: Beta-lactamase TEM
D: Beta-lactamase inhibitory protein


Theoretical massNumber of molelcules
Total (without water)93,1114
Polymers93,1114
Non-polymers00
Water8,431468
1
A: Beta-lactamase TEM
B: Beta-lactamase inhibitory protein


Theoretical massNumber of molelcules
Total (without water)46,5562
Polymers46,5562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-10 kcal/mol
Surface area16240 Å2
MethodPISA
2
C: Beta-lactamase TEM
D: Beta-lactamase inhibitory protein


Theoretical massNumber of molelcules
Total (without water)46,5562
Polymers46,5562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-10 kcal/mol
Surface area16330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.960, 105.220, 82.070
Angle α, β, γ (deg.)90.000, 96.190, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Beta-lactamase TEM / IRT-4 / Penicillinase / TEM-1 / TEM-16/CAZ-7 / TEM-2 / TEM-24/CAZ-6 / TEM-3 / TEM-4 / TEM-5 / TEM-6 ...IRT-4 / Penicillinase / TEM-1 / TEM-16/CAZ-7 / TEM-2 / TEM-24/CAZ-6 / TEM-3 / TEM-4 / TEM-5 / TEM-6 / TEM-8/CAZ-2


Mass: 28941.994 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bla, blaT-3, blaT-4, blaT-5, blaT-6 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P62593, beta-lactamase
#2: Protein Beta-lactamase inhibitory protein / BLIP


Mass: 17613.588 Da / Num. of mol.: 2 / 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.: 468 / 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: 2.26 Å3/Da / Density % sol: 45.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M magnesium chloride, 0.1 M sodium acetate pH 4.6, 25% (w/v) PEG 400

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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: 1.78→38.04 Å / Num. obs: 75080 / % possible obs: 94.79 % / Redundancy: 2.1 % / Biso Wilson estimate: 17.43 Å2 / CC1/2: 0.976 / CC star: 0.994 / Rmerge(I) obs: 0.0532 / Net I/σ(I): 8.92
Reflection shellResolution: 1.78→1.8 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.41 / Num. unique obs: 2530 / CC1/2: 0.862 / CC star: 0.962 / % possible all: 88

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→38.04 Å / SU ML: 0.1815 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.6819
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.215 3771 5.04 %
Rwork0.1762 71111 -
obs0.1781 74882 94.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.61 Å2
Refinement stepCycle: LAST / Resolution: 1.78→38.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6529 0 0 468 6997
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00586659
X-RAY DIFFRACTIONf_angle_d0.83239033
X-RAY DIFFRACTIONf_chiral_restr0.04961017
X-RAY DIFFRACTIONf_plane_restr0.00721171
X-RAY DIFFRACTIONf_dihedral_angle_d14.93612403
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.80.31251390.22712391X-RAY DIFFRACTION88
1.8-1.830.27551340.21482540X-RAY DIFFRACTION90.98
1.83-1.850.24031120.19482616X-RAY DIFFRACTION93.91
1.85-1.880.25611520.21332617X-RAY DIFFRACTION94.18
1.88-1.910.29151510.22062572X-RAY DIFFRACTION94.45
1.91-1.940.35161390.26282551X-RAY DIFFRACTION91.78
1.94-1.970.23131260.2152633X-RAY DIFFRACTION94.1
1.97-20.25181410.1922623X-RAY DIFFRACTION95.38
2-2.040.24051480.17562621X-RAY DIFFRACTION94.57
2.04-2.080.24461450.19982607X-RAY DIFFRACTION94.86
2.08-2.120.22911570.17522608X-RAY DIFFRACTION93.79
2.12-2.170.17791600.15722634X-RAY DIFFRACTION96.11
2.17-2.220.21511470.16512573X-RAY DIFFRACTION93.15
2.22-2.270.21571440.19242587X-RAY DIFFRACTION93.78
2.27-2.330.21931270.17142640X-RAY DIFFRACTION93.54
2.33-2.40.20431200.17132707X-RAY DIFFRACTION98.43
2.4-2.480.21821540.1712638X-RAY DIFFRACTION95.06
2.48-2.570.24381300.17042696X-RAY DIFFRACTION95.34
2.57-2.670.20521560.17542681X-RAY DIFFRACTION98.34
2.67-2.790.21951460.17362653X-RAY DIFFRACTION95.99
2.79-2.940.21871320.17132711X-RAY DIFFRACTION96.6
2.94-3.120.2131270.17682657X-RAY DIFFRACTION95.38
3.12-3.360.21581310.16622644X-RAY DIFFRACTION94.48
3.36-3.70.19821410.16692700X-RAY DIFFRACTION96.17
3.7-4.240.19361230.1592715X-RAY DIFFRACTION96.7
4.24-5.330.17391400.15452761X-RAY DIFFRACTION97.78
5.34-38.040.18731490.182735X-RAY DIFFRACTION96.45

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