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- PDB-9v4a: Crystal Structure of Xeruborbactam (QPX7728) in complex with SME-... -

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Basic information

Entry
Database: PDB / ID: 9v4a
TitleCrystal Structure of Xeruborbactam (QPX7728) in complex with SME-1 class A carbapenemase
ComponentsBeta-lactamase SME-1
KeywordsHYDROLASE / Boronic acid / complex / 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
Chem-RM9 / Beta-lactamase SME-1
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDhankhar, K. / Baidya, S. / Hazra, S.
Funding support India, 2items
OrganizationGrant numberCountry
Board of Research in Nuclear Sciences (BRNS)54/14/03/2023-BRNS India
Indian Council of Medical Research India
CitationJournal: Biochemistry / Year: 2025
Title: Structural Insights into the Role of the Stereochemistry of the Cyclopropyl Ring in the Inhibitory Activity of Xeruborbactam against SME-1 Class A Carbapenemase.
Authors: Dhankhar, K. / S R Nair, A. / Hazra, M. / Alhmeidi Alkhatib, A.E. / Baidya, S. / Mishra, N.C. / Hazra, S.
History
DepositionMay 23, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase SME-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7585
Polymers30,4031
Non-polymers3554
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area10970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.266, 50.505, 60.484
Angle α, β, γ (deg.)90, 98.534, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase SME-1


Mass: 30403.297 Da / Num. of mol.: 1
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-RM9 / (1aR,7bS)-5-fluoro-2-hydroxy-1,1a,2,7b-tetrahydrocyclopropa[c][1,2]benzoxaborinine-4-carboxylic acid


Mass: 221.978 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H8BFO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 1.8 Å3/Da / Density % sol: 31.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Lithium Chloride, 20 % PEG 4000

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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: Sep 11, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.4→25.747 Å / Num. obs: 8582 / % possible obs: 99.9 % / Redundancy: 8.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.124 / Net I/σ(I): 14.4
Reflection shellResolution: 2.4→2.49 Å / Num. unique obs: 866 / CC1/2: 0.933

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
CrysalisProdata reduction
CrysalisProdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→25.747 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.857 / SU B: 9.663 / SU ML: 0.225 / Cross valid method: FREE R-VALUE / ESU R Free: 0.336
RfactorNum. reflection% reflection
Rfree0.2694 425 4.959 %
Rwork0.1768 8146 -
all0.181 --
obs-8571 99.883 %
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: 23.924 Å2
Baniso -1Baniso -2Baniso -3
1--1.005 Å2-0 Å2-1.174 Å2
2---0.099 Å20 Å2
3---1.394 Å2
Refinement stepCycle: LAST / Resolution: 2.4→25.747 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2062 0 22 36 2120
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122119
X-RAY DIFFRACTIONr_angle_refined_deg1.9951.822857
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6035266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg19.64519
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.34910375
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.7171093
X-RAY DIFFRACTIONr_chiral_restr0.1370.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021605
X-RAY DIFFRACTIONr_nbd_refined0.2320.21025
X-RAY DIFFRACTIONr_nbtor_refined0.310.21453
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2120.297
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3280.241
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1140.25
X-RAY DIFFRACTIONr_mcbond_it2.1662.2511067
X-RAY DIFFRACTIONr_mcangle_it3.3994.0371332
X-RAY DIFFRACTIONr_scbond_it2.9972.4921052
X-RAY DIFFRACTIONr_scangle_it4.554.4461522
X-RAY DIFFRACTIONr_lrange_it7.70427.0543318
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
2.4-2.4620.34300.2125700.2196000.930.9721000.193
2.462-2.5290.391310.2175850.2256160.8850.971000.2
2.529-2.6010.271280.2095780.2126060.9470.9721000.189
2.601-2.6810.337260.2065370.2125630.9410.9741000.185
2.681-2.7670.271320.1965280.25600.9660.9761000.178
2.767-2.8630.35310.1975090.2065400.9190.9751000.178
2.863-2.970.275390.1954900.25290.9620.9751000.177
2.97-3.090.302210.2064740.2094950.9410.9711000.192
3.09-3.2250.298210.1924610.1974820.9380.9771000.18
3.225-3.380.266240.194420.1944670.9660.97999.78590.18
3.38-3.5590.259270.1694170.1744440.9610.9831000.159
3.559-3.770.184290.1633920.1644210.9760.9831000.156
3.77-4.0250.298180.1513840.1564020.950.9861000.144
4.025-4.3380.278160.1563410.1613570.9640.9851000.15
4.338-4.7390.175120.1423300.1433420.9860.9871000.14
4.739-5.2760.198160.1413010.1443170.9810.9871000.138
5.276-6.050.222110.1812740.1832850.9790.9791000.17
6.05-7.3090.33970.1782270.1812340.8760.9811000.171
7.309-9.9440.43430.1291840.1331870.9760.9891000.127
9.944-25.7470.13430.1371220.1371260.9810.98899.20630.138

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