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- PDB-9vgv: Crystal Structure of BlaA beta-lactamase in complex with the Anti... -

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Basic information

Entry
Database: PDB / ID: 9vgv
TitleCrystal Structure of BlaA beta-lactamase in complex with the Antifungal Agent Tavaborole.
ComponentsBeta-lactamase
KeywordsHYDROLASE / Acyl Enzyme complex / beta-lactamase inhibitor / Transition state analogue / Complex crystal structure
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
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
Biological speciesYersinia enterocolitica (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDhankhar, K. / Bhattacharya, S. / Hazra, S.
Funding support India, 2items
OrganizationGrant numberCountry
Indian Council of Medical ResearchEM/Dev/IG/20/07/73/2023 India
Board of Research in Nuclear Sciences (BRNS)54/14/03/2023-BRNS/12162 India
CitationJournal: To Be Published
Title: Crystal Structure of BlaA beta-lactamase in complex with the Antifungal Agent Tavaborole.
Authors: Dhankhar, K. / Bhattacharya, S. / Hazra, S.
History
DepositionJun 15, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 6, 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)28,6523
Polymers28,4641
Non-polymers1872
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-5 kcal/mol
Surface area11370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.494, 72.98, 43.938
Angle α, β, γ (deg.)90, 94.421, 90
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-437-

HOH

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Components

#1: Protein Beta-lactamase / Penicillinase


Mass: 28464.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia enterocolitica (bacteria) / Gene: blaA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q01166, beta-lactamase
#2: Chemical ChemComp-A1CF8 / Tavaborole / 5-fluoro-2,1-benzoxaborol-1(3H)-ol


Mass: 151.931 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6BFO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.57 Å3/Da / Density % sol: 52.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M TRIS hydrochloride pH 8.5, 2.0 M Ammonium phosphate monobasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Aug 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2.5→24.44 Å / Num. obs: 10042 / % possible obs: 99.9 % / Redundancy: 6.2 % / CC1/2: 0.998 / Net I/σ(I): 7.8
Reflection shellResolution: 2.5→2.6 Å / Num. unique obs: 1134 / CC1/2: 0.925 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
CrysalisProdata reduction
CrysalisProdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8IWV

8iwv


Resolution: 2.5→23.516 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.841 / SU B: 10.89 / SU ML: 0.243 / Cross valid method: FREE R-VALUE / ESU R: 0.624 / ESU R Free: 0.318 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2694 474 4.721 %
Rwork0.1966 9566 -
all0.2 --
obs-10040 99.801 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 24.761 Å2
Baniso -1Baniso -2Baniso -3
1-2.364 Å20 Å20.147 Å2
2---0.679 Å20 Å2
3----1.687 Å2
Refinement stepCycle: LAST / Resolution: 2.5→23.516 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1992 0 12 37 2041
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122062
X-RAY DIFFRACTIONr_angle_refined_deg2.1571.8092803
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3995263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.762517
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.17710347
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.3061090
X-RAY DIFFRACTIONr_chiral_restr0.1380.2321
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021572
X-RAY DIFFRACTIONr_nbd_refined0.2390.2916
X-RAY DIFFRACTIONr_nbtor_refined0.3170.21405
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.282
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2110.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0430.23
X-RAY DIFFRACTIONr_mcbond_it2.0752.3041049
X-RAY DIFFRACTIONr_mcangle_it3.3144.1291313
X-RAY DIFFRACTIONr_scbond_it3.5892.6071013
X-RAY DIFFRACTIONr_scangle_it5.7814.6371490
X-RAY DIFFRACTIONr_lrange_it7.20825.9533073
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.5-2.5640.28420.2166770.2197190.930.9671000.207
2.564-2.6340.294330.226880.2247210.9450.9691000.214
2.634-2.7090.322400.1946540.2016940.9280.9731000.183
2.709-2.7910.322350.2146480.2196830.9310.9711000.207
2.791-2.8810.339370.1995990.2076360.9230.9741000.19
2.881-2.9810.291260.2276120.236380.9460.9661000.217
2.981-3.0920.322200.2076010.2116210.9410.9711000.2
3.092-3.2150.312190.2015610.2045800.9440.9731000.193
3.215-3.3560.249310.1895370.1925680.9620.9761000.185
3.356-3.5160.234230.175150.1735380.9640.9821000.166
3.516-3.7010.253170.175040.1735220.9570.98299.80840.174
3.701-3.920.244150.1844810.1864960.9550.9771000.187
3.92-4.1820.294210.1934500.1974710.9530.9771000.198
4.182-4.5050.211290.1853880.1874170.9710.9771000.189
4.505-4.9170.214200.1873900.1884100.9740.9771000.194
4.917-5.4680.319190.2143390.2193580.920.9711000.223
5.468-6.2580.256150.2323030.2333190.9780.9799.68650.239
6.258-7.5320.204150.1952690.1962840.9740.9751000.196
7.532-10.1440.280.1562140.1582220.9810.9821000.164
10.144-23.5160.32390.2441350.2471500.9690.966960.262

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