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- PDB-9jnb: Crystal Structure of SME-1 E166A mutant in complex with imipenem -

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Basic information

Entry
Database: PDB / ID: 9jnb
TitleCrystal Structure of SME-1 E166A mutant in complex with imipenem
Componentsbeta-lactamase
KeywordsHYDROLASE / Class A Carbapenemase / Imipenem / AMR
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
Imipenem / Beta-lactamase SME-1
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDhankhar, K. / 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: To Be Published
Title: Crystal Structure of SME-1 E166A mutant in complex with imipenem
Authors: Dhankhar, K. / Hazra, S.
History
DepositionSep 23, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8182
Polymers29,5161
Non-polymers3011
Water1,49583
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.847, 50.915, 60.835
Angle α, β, γ (deg.)90, 98.935, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein beta-lactamase / SME-1 E166A


Mass: 29516.395 Da / Num. of mol.: 1 / Mutation: E166A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Gene: sme-2, blaSME-1, blaSME-4, blaSME1, SME12620_22 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q54488, beta-lactamase
#2: Chemical ChemComp-ID1 / Imipenem


Mass: 301.362 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N3O4S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 1.92 Å3/Da / Density % sol: 35.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 4000, 0.2M Lithium chloride

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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 15, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→25.3 Å / Num. obs: 11402 / % possible obs: 99.8 % / Redundancy: 7 % / CC1/2: 0.996 / Net I/σ(I): 13.7
Reflection shellResolution: 2.2→2.27 Å / Num. unique obs: 10727 / CC1/2: 0.937

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
CrysalisProdata reduction
CrysalisProdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→23.452 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.85 / SU B: 19.98 / SU ML: 0.221 / Cross valid method: FREE R-VALUE / ESU R Free: 0.283 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2826 534 4.683 %
Rwork0.1996 10868 -
all0.203 --
obs-11402 99.642 %
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: 21.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.645 Å20 Å2-1.659 Å2
2--1.216 Å20 Å2
3----0.047 Å2
Refinement stepCycle: LAST / Resolution: 2.2→23.452 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2054 0 20 83 2157
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0122131
X-RAY DIFFRACTIONr_angle_refined_deg1.671.8232870
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1835266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.498521
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.02110369
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.2591092
X-RAY DIFFRACTIONr_chiral_restr0.1140.2318
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021599
X-RAY DIFFRACTIONr_nbd_refined0.2230.21032
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21445
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2030.2122
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.230.226
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3240.24
X-RAY DIFFRACTIONr_mcbond_it4.3972.0181067
X-RAY DIFFRACTIONr_mcangle_it7.0423.6221332
X-RAY DIFFRACTIONr_scbond_it5.2992.1881064
X-RAY DIFFRACTIONr_scangle_it8.1823.9371538
X-RAY DIFFRACTIONr_lrange_it13.4321.9623309
X-RAY DIFFRACTIONr_rigid_bond_restr3.41332131
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
2.2-2.2570.315400.2557910.2578310.9240.9611000.249
2.257-2.3180.251350.2137880.2158230.9540.9671000.211
2.318-2.3850.278430.1867250.1917680.9430.9751000.18
2.385-2.4570.34390.197430.1977820.9350.9791000.186
2.457-2.5370.407290.2157210.2217500.9170.9771000.208
2.537-2.6250.288460.2356720.2397180.9560.9751000.222
2.625-2.7230.308330.2446430.2486760.9440.9771000.223
2.723-2.8320.495380.2516510.2636970.9170.97498.85220.227
2.832-2.9560.493280.2855920.2936230.8970.95999.51850.253
2.956-3.0980.288230.2545890.2556170.9550.96299.18960.226
3.098-3.2620.284310.2095580.2135890.950.981000.197
3.262-3.4560.259330.2215320.2235660.9680.98799.82330.214
3.456-3.6890.19190.1915170.1915360.980.9891000.182
3.689-3.9760.246220.1484570.1524810.9650.9999.58420.14
3.976-4.3430.248150.1464310.1494500.9280.98799.11110.133
4.343-4.8350.143130.1373970.1374150.9880.9998.79520.13
4.835-5.5440.307170.163540.1653730.9480.98599.46380.151
5.544-6.6970.379130.2043010.2113140.9350.9811000.197
6.697-9.1070.156120.1572470.1572590.9830.991000.154
9.107-23.4520.08350.1551580.15316310.991000.154

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