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- PDB-9jne: Crystal Structure of SME-1 E166A mutant in complex with Doripenem -

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Basic information

Entry
Database: PDB / ID: 9jne
TitleCrystal Structure of SME-1 E166A mutant in complex with Doripenem
Componentsbeta-lactamase
KeywordsHYDROLASE / Acyl Enzyme Complex / Carbapenemase / DBO
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-DRW / DI(HYDROXYETHYL)ETHER / Beta-lactamase SME-1
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDhankhar, K. / Hazra, S.
Funding support India, 2items
OrganizationGrant numberCountry
Indian Council of Medical ResearchEM/Dev/IG/20/0773/2023 India
Board of Research in Nuclear Sciences (BRNS)54/14/03/2023-BRNS India
CitationJournal: To Be Published
Title: Crystal Structure of SME-1 E166A mutant in complex with Doripenem
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

Downloads & links

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Assembly

Deposited unit
A: beta-lactamase
B: beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9427
Polymers60,6912
Non-polymers1,2525
Water2,270126
1
A: beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9804
Polymers30,3451
Non-polymers6353
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9623
Polymers30,3451
Non-polymers6172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.743, 51.768, 75.004
Angle α, β, γ (deg.)90, 114.216, 90
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: ASP / End label comp-ID: ASP / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 1 - 267 / Label seq-ID: 3 - 269

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein beta-lactamase / SME E166A


Mass: 30345.266 Da / Num. of mol.: 2
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-DRW / (2S,3R,4S)-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-methyl-4-({(3S,5S)-5-[(sulfamoylamino)methyl]pyrrolidin-3-yl}sulfanyl)-3,4-dihydro-2H-pyrrole-5-carboxylic acid / Doripenem(open form, pyrroline tautomer form 2, SP3 connection to Thio as S isomer)


Mass: 422.520 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H26N4O6S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.16 Å3/Da / Density % sol: 41.23 %
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 23, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→28.553 Å / Num. obs: 17497 / % possible obs: 99.2 % / Redundancy: 7.9 % / CC1/2: 0.996 / Net I/σ(I): 16.6
Reflection shellResolution: 2.5→2.6 Å / Num. unique obs: 1981 / CC1/2: 0.994

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
CrysalisProdata reduction
CrysalisProdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→28.553 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.854 / SU B: 26.712 / SU ML: 0.269 / Cross valid method: FREE R-VALUE / ESU R Free: 0.38 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2913 907 5.188 %
Rwork0.209 16575 -
all0.213 --
obs-17482 99.071 %
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: 9.364 Å2
Baniso -1Baniso -2Baniso -3
1-0.826 Å20 Å2-0.643 Å2
2---0.202 Å20 Å2
3----0.033 Å2
Refinement stepCycle: LAST / Resolution: 2.5→28.553 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4108 0 81 126 4315
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0124268
X-RAY DIFFRACTIONr_angle_refined_deg2.5491.825752
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4965534
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.496534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.64710739
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.19310184
X-RAY DIFFRACTIONr_chiral_restr0.170.2638
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023190
X-RAY DIFFRACTIONr_nbd_refined0.2380.21999
X-RAY DIFFRACTIONr_nbtor_refined0.3150.22943
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2060.2199
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2740.242
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3870.22
X-RAY DIFFRACTIONr_mcbond_it7.5410.7672139
X-RAY DIFFRACTIONr_mcangle_it11.0091.372672
X-RAY DIFFRACTIONr_scbond_it3.8390.9072129
X-RAY DIFFRACTIONr_scangle_it6.0111.6263080
X-RAY DIFFRACTIONr_lrange_it24.5778.8746513
X-RAY DIFFRACTIONr_rigid_bond_restr4.46134268
X-RAY DIFFRACTIONr_ncsr_local_group_10.0830.058816
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.082610.05009
12AX-RAY DIFFRACTIONLocal ncs0.082610.05009
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
2.5-2.5640.325690.20912230.21512920.9280.9751000.192
2.564-2.6340.383580.20911690.21712270.9260.9751000.196
2.634-2.710.279580.20311600.20712200.9510.97899.83610.19
2.71-2.7920.314790.1911100.19811900.9450.9899.9160.178
2.792-2.8830.366680.23511010.24411700.9140.96699.91450.222
2.883-2.9830.346610.22810330.23510950.9190.96799.90870.216
2.983-3.0950.358430.22210170.22810610.9180.96999.90570.211
3.095-3.2190.273450.239970.23210460.9520.96899.61760.226
3.219-3.360.304500.2359410.2389960.9480.96799.4980.233
3.36-3.5220.233440.2188950.2199500.970.97698.84210.216
3.522-3.7090.276410.2368460.2389060.9460.97397.90290.23
3.709-3.930.28450.2138040.2178610.9660.97698.60630.216
3.93-4.1960.264380.1827590.1868180.9610.9897.43280.181
4.196-4.5240.19350.1597090.1617560.9840.98698.41270.163
4.524-4.9430.262240.1746530.1777000.9630.98696.71430.179
4.943-5.5060.332260.2056010.216340.9230.97998.89590.208
5.506-6.3190.289330.2225350.2275730.9770.97799.12740.221
6.319-7.6460.258480.1974400.2044900.9740.98499.59180.205
7.646-10.4450.206260.1553620.1583960.9830.98897.97980.172
10.445-28.5530.272160.2342200.2372500.9810.98194.40.247

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