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- PDB-9v49: Crystal Structure of 2R, 3S-Xeruborbactam with SME-1 -

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Basic information

Entry
Database: PDB / ID: 9v49
TitleCrystal Structure of 2R, 3S-Xeruborbactam with SME-1
ComponentsBeta-lactamase SME-1
KeywordsHYDROLASE / Stereo isomer / Xeruborbactam / 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
: / DI(HYDROXYETHYL)ETHER / Beta-lactamase SME-1
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 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 ResearchEM/DEV/IG/20/0773/2023 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

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)61,96314
Polymers60,8072
Non-polymers1,15712
Water1,874104
1
A: Beta-lactamase SME-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1749
Polymers30,4031
Non-polymers7708
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-12 kcal/mol
Surface area11060 Å2
MethodPISA
2
B: Beta-lactamase SME-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7905
Polymers30,4031
Non-polymers3874
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.98, 51.237, 74.856
Angle α, β, γ (deg.)90, 113.404, 90
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Beta-lactamase SME-1


Mass: 30403.297 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

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Non-polymers , 6 types, 116 molecules

#2: Chemical ChemComp-A1MAF / (1~{a}~{S},7~{b}~{R})-5-fluoranyl-2-oxidanyl-1~{a},7~{b}-dihydro-1~{H}-cyclopropa[c][1,2]benzoxaborinine-4-carboxylic acid / (1R,2S)-Xeruborbactam disodium


Mass: 221.978 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H8BFO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.05 Å3/Da / Density % sol: 40.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M 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 10, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→23.683 Å / Num. obs: 25335 / % possible obs: 99.9 % / Redundancy: 7.4 % / CC1/2: 0.996 / Net I/σ(I): 11.2
Reflection shellResolution: 2.2→2.27 Å / Num. unique obs: 2174 / CC1/2: 0.753

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
CrysalisProdata reduction
CrysalisProdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→23.683 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.9 / SU B: 7.827 / SU ML: 0.188 / Cross valid method: FREE R-VALUE / ESU R: 0.332 / ESU R Free: 0.236
RfactorNum. reflection% reflection
Rfree0.2492 1261 4.98 %
Rwork0.187 24061 -
all0.19 --
obs-25322 99.89 %
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: 20.912 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å2-0 Å2-0.425 Å2
2---0.62 Å20 Å2
3---1.119 Å2
Refinement stepCycle: LAST / Resolution: 2.2→23.683 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4116 0 72 104 4292
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0124264
X-RAY DIFFRACTIONr_angle_refined_deg2.1551.8215743
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3325534
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.3056.76534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.21110744
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.80210187
X-RAY DIFFRACTIONr_chiral_restr0.1490.2627
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023214
X-RAY DIFFRACTIONr_nbd_refined0.2320.22014
X-RAY DIFFRACTIONr_nbtor_refined0.310.22905
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.2200
X-RAY DIFFRACTIONr_metal_ion_refined0.2480.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2750.263
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1940.26
X-RAY DIFFRACTIONr_mcbond_it1.8591.9252139
X-RAY DIFFRACTIONr_mcangle_it2.8893.4492672
X-RAY DIFFRACTIONr_scbond_it32.1852125
X-RAY DIFFRACTIONr_scangle_it4.6223.8643065
X-RAY DIFFRACTIONr_lrange_it6.46423.0976562
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
2.2-2.2570.337730.28217630.28518380.9280.94299.89120.268
2.257-2.3180.26700.23617290.23717990.950.9611000.221
2.318-2.3840.317630.25216720.25517350.9290.9541000.235
2.384-2.4570.3910.23416130.23817040.9360.9621000.212
2.457-2.5370.321840.22315580.22716420.9310.9691000.2
2.537-2.6250.261790.19915150.20215940.9630.9761000.174
2.625-2.7220.314940.20714630.21315570.940.9741000.178
2.722-2.8320.247650.18814380.1915030.9620.981000.162
2.832-2.9560.29910.20613290.21114200.9490.9731000.179
2.956-3.0980.247690.1912890.19313580.9550.9771000.163
3.098-3.2620.278570.19712490.213060.940.9761000.173
3.262-3.4560.24560.17611740.17812300.9640.9821000.159
3.456-3.6890.191480.16511230.16611710.9780.9851000.151
3.689-3.9770.217620.15210490.15511110.9730.9871000.14
3.977-4.3440.19510.1399360.1419870.980.9891000.129
4.344-4.8370.198760.1358320.149090.9790.9999.890.125
4.837-5.5460.255420.1447830.1498250.9650.9881000.132
5.546-6.7020.201350.1626720.1637070.9770.9861000.144
6.702-9.1190.16350.1515250.1525600.9810.9881000.148
9.119-23.6830.376200.153490.1563700.9220.98999.72970.149

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