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- PDB-9w7n: Crystal Structure of Vaborbactam in complex with SME-1 class A Ca... -

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Basic information

Entry
Database: PDB / ID: 9w7n
TitleCrystal Structure of Vaborbactam in complex with SME-1 class A Carbapenemase
ComponentsBeta-lactamase SME-1
KeywordsHYDROLASE / Boronic acid / Transition state analogue / Inhibitor
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
Vaborbactam / Beta-lactamase SME-1
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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)59,8177
Polymers58,7722
Non-polymers1,0455
Water4,270237
1
A: Beta-lactamase SME-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9404
Polymers29,3861
Non-polymers5533
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase SME-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8783
Polymers29,3861
Non-polymers4912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.039, 51.011, 130.533
Angle α, β, γ (deg.)90, 92.799, 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-4D6 / Vaborbactam / {(3R,6S)-2-hydroxy-3-[(thiophen-2-ylacetyl)amino]-1,2-oxaborinan-6-yl}acetic acid / 2-((3R,6S)-2-hydroxy-3-(2-(thiophen-2-yl)acetamido)-1,2-oxaborinan-6-yl)acetic acid / 2-[(3R,6S)-2-hydroxy-3-[(2-thiophen-2-ylacetyl)amino]oxaborinan-6-yl]acetic acid / 1,2-Oxaborinane-6-acetic acid, 2-hydroxy-3-((2-(2-thienyl)acetyl)amino)-, (3R,6S)-


Mass: 297.135 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C12H16BNO5S / 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: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.04 Å3/Da / Density % sol: 39.68 %
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: Jul 29, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→23.92 Å / Num. obs: 32253 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.996 / Net I/σ(I): 14.7
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 2304 / CC1/2: 0.898

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
CrysalisProdata reduction
CrysalisProdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→23.764 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.887 / SU B: 12.326 / SU ML: 0.15 / Cross valid method: FREE R-VALUE / ESU R Free: 0.188 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2418 1604 4.975 %
Rwork0.1849 30636 -
all0.188 --
obs-32240 99.827 %
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: 14.347 Å2
Baniso -1Baniso -2Baniso -3
1-2.094 Å20 Å20.271 Å2
2--1.881 Å20 Å2
3----3.983 Å2
Refinement stepCycle: LAST / Resolution: 2→23.764 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4123 0 70 237 4430
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124330
X-RAY DIFFRACTIONr_angle_refined_deg1.9281.8255834
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8795546
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.532534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.95710758
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.85910191
X-RAY DIFFRACTIONr_chiral_restr0.1260.2635
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023264
X-RAY DIFFRACTIONr_nbd_refined0.2260.22213
X-RAY DIFFRACTIONr_nbtor_refined0.3090.22979
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.2308
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2940.262
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2190.220
X-RAY DIFFRACTIONr_mcbond_it2.2681.2032148
X-RAY DIFFRACTIONr_mcangle_it3.7212.1632685
X-RAY DIFFRACTIONr_scbond_it2.971.3262182
X-RAY DIFFRACTIONr_scangle_it4.5192.3773142
X-RAY DIFFRACTIONr_lrange_it27.08415.2796951
X-RAY DIFFRACTIONr_rigid_bond_restr5.3634330
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
2-2.0510.2781200.20421700.20823170.950.97698.83470.193
2.051-2.1070.3071310.20221850.20723160.9460.9761000.187
2.107-2.1680.2861120.20320900.20722020.9340.9761000.187
2.168-2.2340.2881060.19321090.19822150.9470.9781000.176
2.234-2.3060.277810.17820210.18221020.9480.9821000.162
2.306-2.3860.2471010.18719360.1920370.9620.981000.171
2.386-2.4760.269880.19318660.19719540.9530.9781000.177
2.476-2.5760.223840.18418340.18619180.9680.9811000.168
2.576-2.6890.246890.18917130.19118020.9550.9791000.172
2.689-2.8180.2191040.19816480.19917520.9630.9761000.185
2.818-2.9680.31970.2115770.21516740.9360.9711000.195
2.968-3.1450.292940.20314680.20815620.9410.9731000.192
3.145-3.3580.235800.20314010.20514810.9660.9751000.194
3.358-3.6210.225720.18713410.18914130.9720.9811000.183
3.621-3.9580.223490.16112250.16312740.9760.9851000.158
3.958-4.4090.153640.1510930.1511570.9840.9881000.15
4.409-5.0630.147330.14210090.14310420.9860.9891000.143
5.063-6.1310.256350.1958530.1978880.9660.9821000.192
6.131-8.3960.14300.156790.157090.9890.991000.151
8.396-23.7640.17340.1584160.1594540.9820.98799.11890.157

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