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- PDB-9vxs: Crystal structure of Antifungal agent Tavaborole in complex with ... -

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Basic information

Entry
Database: PDB / ID: 9vxs
TitleCrystal structure of Antifungal agent Tavaborole in complex with SME-1 class A carbapenemase
ComponentsBeta-lactamase SME-1
KeywordsANTIMICROBIAL PROTEIN / Tavaborole / inhibitor / carbapenemase
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, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
: / DI(HYDROXYETHYL)ETHER / Beta-lactamase SME-1
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDhankhar, K. / Hazra, S.
Funding support India, 2items
OrganizationGrant numberCountry
Indian Council of Medical Research India
Board of Research in Nuclear Sciences (BRNS) India
CitationJournal: To Be Published
Title: Crystal structure of Antifungal agent Tavaborole in complex with SME-1 class A carbapenemase
Authors: Dhankhar, K. / Hazra, S.
History
DepositionJul 20, 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
B: Beta-lactamase SME-1
A: Beta-lactamase SME-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3229
Polymers58,7722
Non-polymers5507
Water2,000111
1
B: Beta-lactamase SME-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6433
Polymers29,3861
Non-polymers2572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11130 Å2
MethodPISA
2
A: Beta-lactamase SME-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6796
Polymers29,3861
Non-polymers2935
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-13 kcal/mol
Surface area11190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.235, 51.153, 78.318
Angle α, β, γ (deg.)90, 114.896, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase SME-1


Mass: 29386.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria)
Gene: SME-1, blaSME-1, blaSME-4, blaSME1, bpl-1, bplA, sme-2, smeA
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P52682, beta-lactamase
#2: Chemical ChemComp-A1II0 / 3-fluoranyl-7-oxidanyl-8-oxa-7$l^{4}-borabicyclo[4.3.0]nona-1(9),2,4,6-tetraene


Mass: 150.923 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H5BFO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.23 Å3/Da / Density % sol: 44.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M lithium chloride, PEG 4000 20%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jul 2, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→29.502 Å / Num. obs: 18229 / % possible obs: 99.9 % / Redundancy: 9.6 % / CC1/2: 0.992 / Net I/σ(I): 10.8
Reflection shellResolution: 2.5→2.6 Å / Num. unique obs: 2060 / CC1/2: 0.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
CrysalisProdata reduction
CrysalisProdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→29.502 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.86 / SU B: 11.207 / SU ML: 0.242 / Cross valid method: FREE R-VALUE / ESU R: 2.093 / ESU R Free: 0.339
RfactorNum. reflection% reflection
Rfree0.2684 917 5.035 %
Rwork0.188 17295 -
all0.192 --
obs-18212 99.781 %
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: 18.669 Å2
Baniso -1Baniso -2Baniso -3
1--0.508 Å2-0 Å2-0.8 Å2
2---1.092 Å2-0 Å2
3---1.637 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.502 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4124 0 33 111 4268
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0124226
X-RAY DIFFRACTIONr_angle_refined_deg2.0251.8175693
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5715532
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.032534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.06610750
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.46610186
X-RAY DIFFRACTIONr_chiral_restr0.1480.2620
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023200
X-RAY DIFFRACTIONr_nbd_refined0.2270.21984
X-RAY DIFFRACTIONr_nbtor_refined0.310.22880
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2211
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.270.236
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1950.25
X-RAY DIFFRACTIONr_mcbond_it1.5411.7272134
X-RAY DIFFRACTIONr_mcangle_it2.5283.0962664
X-RAY DIFFRACTIONr_scbond_it2.6961.9652092
X-RAY DIFFRACTIONr_scangle_it4.3893.4823029
X-RAY DIFFRACTIONr_lrange_it6.10318.5016490
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
2.5-2.5640.287670.23612690.23913370.9440.96699.92520.213
2.564-2.6340.346650.22712090.23312740.9270.9691000.2
2.634-2.710.375760.20511960.21512720.9460.9751000.181
2.71-2.7930.29640.20511620.20912260.950.9741000.174
2.793-2.8830.314500.21211350.21711850.9450.9731000.18
2.883-2.9840.33750.22610700.23311450.9320.9671000.197
2.984-3.0950.324610.22910570.23411180.9290.9631000.202
3.095-3.220.304510.20910180.21410690.9420.9721000.183
3.22-3.3610.287550.1989670.20310220.9540.9791000.181
3.361-3.5230.254500.2049340.2079840.9560.9791000.187
3.523-3.7110.211400.1889120.1889520.9770.9861000.174
3.711-3.9320.248480.1728360.1768860.9650.98699.77430.153
3.932-4.1980.239370.1538000.1568370.9560.9871000.132
4.198-4.5270.25460.1567340.1617800.9660.9861000.141
4.527-4.9470.189250.1426990.1447270.9820.98999.58730.123
4.947-5.5120.257300.1576360.1616660.9630.9861000.132
5.512-6.3280.156220.1655690.1655910.9880.9861000.143
6.328-7.6620.162180.164790.164970.9830.9891000.141
7.662-10.4880.18320.1293780.1334100.9860.9931000.117
10.488-29.5020.25250.1852350.1862600.9970.98392.30770.17

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