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- PDB-9w7o: Crystal Structure of Taniborbactam in complex with SME-1 class A ... -

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Basic information

Entry
Database: PDB / ID: 9w7o
TitleCrystal Structure of Taniborbactam in complex with SME-1 class A Carbapenemase
ComponentsBeta-lactamase SME-1
KeywordsHYDROLASE / Boronic acid based transition state analogue (Batsa)
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
Chem-KJK / Beta-lactamase SME-1
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.93 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: Org.Biomol.Chem. / Year: 2025
Title: Beyond structure and activity: targeting class A carbapenemases with monocyclic and bicyclic boronic acids to counter antimicrobial resistance.
Authors: Dhankhar, K. / Hazra, M. / Nair, A.S.R. / Alhmeidi Alkhatib, A.E. / Mishra, N.C. / Hazra, S.
History
DepositionAug 6, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 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 SME-1
B: Beta-lactamase SME-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9396
Polymers58,7722
Non-polymers1,1674
Water6,287349
1
A: Beta-lactamase SME-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9703
Polymers29,3861
Non-polymers5832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase SME-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9703
Polymers29,3861
Non-polymers5832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.817, 51.512, 74.697
Angle α, β, γ (deg.)90, 113.075, 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-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.: 2 / Source method: obtained synthetically / Formula: C19H28BN3O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 2.13 Å3/Da / Density % sol: 42.33 %
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 31, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→24.887 Å / Num. obs: 46191 / % possible obs: 99.9 % / Redundancy: 6.1 % / CC1/2: 0.961 / Net I/σ(I): 11.8
Reflection shellResolution: 1.8→1.84 Å / Num. unique obs: 2776 / CC1/2: 0.717

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
CrysalisProdata reduction
CrysalisProdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→24.887 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.905 / SU B: 3.794 / SU ML: 0.111 / Cross valid method: FREE R-VALUE / ESU R: 0.188 / ESU R Free: 0.168
RfactorNum. reflection% reflection
Rfree0.2384 1855 4.944 %
Rwork0.1842 35667 -
all0.187 --
obs-37522 99.88 %
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: 14.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.659 Å2-0 Å2-0.373 Å2
2--0.405 Å2-0 Å2
3----0.548 Å2
Refinement stepCycle: LAST / Resolution: 1.93→24.887 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4120 0 82 349 4551
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0124351
X-RAY DIFFRACTIONr_angle_refined_deg1.9481.8195856
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6425544
X-RAY DIFFRACTIONr_dihedral_angle_2_deg18.447539
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.12410757
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.96810192
X-RAY DIFFRACTIONr_chiral_restr0.1320.2634
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023272
X-RAY DIFFRACTIONr_nbd_refined0.2110.22122
X-RAY DIFFRACTIONr_nbtor_refined0.310.22971
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2320
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2340.273
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.240.217
X-RAY DIFFRACTIONr_mcbond_it1.0981.1772151
X-RAY DIFFRACTIONr_mcangle_it1.7642.1092688
X-RAY DIFFRACTIONr_scbond_it2.1781.4522200
X-RAY DIFFRACTIONr_scangle_it3.3992.5433162
X-RAY DIFFRACTIONr_lrange_it4.86215.3376882
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
1.93-1.980.2581330.19526200.19827530.9560.9741000.181
1.98-2.0340.271400.18625330.1926730.9530.9761000.171
2.034-2.0920.1981170.17724850.17826020.9740.9791000.162
2.092-2.1560.2451180.18324270.18625460.9620.97699.96070.167
2.156-2.2260.2371120.18423260.18624380.9660.9781000.167
2.226-2.3040.2291180.1822460.18323640.9690.9791000.165
2.304-2.390.2531160.18121870.18523030.9610.9791000.166
2.39-2.4870.2651080.18220880.18621960.9590.9791000.166
2.487-2.5960.248880.18920450.19221340.9650.97899.95310.174
2.596-2.7210.3151140.20119110.20720250.9440.9761000.186
2.721-2.8670.279820.2118410.21319230.9520.9731000.197
2.867-3.0380.3171050.20417300.2118350.9360.9731000.194
3.038-3.2440.273920.19616410.217340.9570.97699.94230.19
3.244-3.4990.242890.19915090.20116010.9590.97699.81260.195
3.499-3.8260.217720.17214160.17414900.9710.98399.86580.173
3.826-4.2650.197720.16512730.16713490.9780.98699.70350.169
4.265-4.90.143590.14211390.14212050.9880.98999.41910.15
4.9-5.9440.185630.179750.17110400.9770.98399.80770.173
5.944-8.1770.153330.1867860.1848190.990.9841000.186
8.177-24.8870.255240.2034880.2055150.9510.98299.41750.209

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