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- PDB-9ujb: Crystal Structure of SME-1 E166A in complex with Ceftobiprole -

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Basic information

Entry
Database: PDB / ID: 9ujb
TitleCrystal Structure of SME-1 E166A in complex with Ceftobiprole
ComponentsBeta-lactamase SME-1
KeywordsHYDROLASE / Carbapenemase / complex
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
PHOSPHATE ION / Chem-RB6 / Beta-lactamase SME-1
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 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: To Be Published
Title: Crystal Structure of SME-1 E166A in complex with Ceftobiprole
Authors: Dhankhar, K. / Hazra, S.
History
DepositionApr 17, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)61,85210
Polymers60,6912
Non-polymers1,1628
Water3,297183
1
A: Beta-lactamase SME-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7055
Polymers30,3451
Non-polymers3604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11110 Å2
MethodPISA
2
B: Beta-lactamase SME-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1475
Polymers30,3451
Non-polymers8024
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-13 kcal/mol
Surface area11190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.503, 51.362, 131.086
Angle α, β, γ (deg.)90, 93.056, 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: 30345.266 Da / Num. of mol.: 2 / Mutation: E166A
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 , 5 types, 191 molecules

#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-RB6 / (2R)-2-[(1R)-1-{[(2Z)-2-(5-amino-1,2,4-thiadiazol-3-yl)-2-(hydroxyimino)acetyl]amino}-2-oxoethyl]-5-({2-oxo-1-[(3R)-pyr rolidin-3-yl]-2,5-dihydro-1H-pyrrol-3-yl}methyl)-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid / BAL 9141, bound form / ceftobiprole, bound form


Mass: 536.585 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N8O6S2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.02 Å3/Da / Density % sol: 39.05 %
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: Jun 26, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→25.68 Å / Num. obs: 28581 / % possible obs: 99.9 % / Redundancy: 7.3 % / CC1/2: 0.996 / Net I/σ(I): 13
Reflection shellResolution: 2.1→2.16 Å / Num. unique obs: 2331 / CC1/2: 0.871

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
CrysalisProdata reduction
CrysalisProdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→25.68 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.907 / SU B: 5.719 / SU ML: 0.152 / Cross valid method: FREE R-VALUE / ESU R: 0.267 / ESU R Free: 0.199 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2331 1340 4.691 %
Rwork0.187 27227 -
all0.189 --
obs-28567 99.909 %
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: 17.648 Å2
Baniso -1Baniso -2Baniso -3
1-1.666 Å2-0 Å2-0.722 Å2
2---0.509 Å2-0 Å2
3----1.074 Å2
Refinement stepCycle: LAST / Resolution: 2.1→25.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4108 0 71 183 4362
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124246
X-RAY DIFFRACTIONr_angle_refined_deg1.8981.8225719
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8955532
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.4017.2540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.41910738
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.58310184
X-RAY DIFFRACTIONr_chiral_restr0.1230.2624
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023206
X-RAY DIFFRACTIONr_nbd_refined0.2260.22014
X-RAY DIFFRACTIONr_nbtor_refined0.3080.22933
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.2252
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2280.258
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2120.210
X-RAY DIFFRACTIONr_mcbond_it1.3891.552134
X-RAY DIFFRACTIONr_mcangle_it2.2092.7782664
X-RAY DIFFRACTIONr_scbond_it2.621.8862112
X-RAY DIFFRACTIONr_scangle_it4.1233.323055
X-RAY DIFFRACTIONr_lrange_it6.02818.6376605
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.1540.2981170.2391971X-RAY DIFFRACTION100
2.154-2.2130.277730.2041928X-RAY DIFFRACTION100
2.213-2.2760.225790.1851937X-RAY DIFFRACTION100
2.276-2.3460.249850.181822X-RAY DIFFRACTION100
2.346-2.4220.24810.1921811X-RAY DIFFRACTION100
2.422-2.5060.241830.1891670X-RAY DIFFRACTION100
2.506-2.60.283800.1911690X-RAY DIFFRACTION100
2.6-2.7050.274880.1891580X-RAY DIFFRACTION100
2.705-2.8240.261770.2011550X-RAY DIFFRACTION100
2.824-2.960.284690.2121450X-RAY DIFFRACTION100
2.96-3.1180.222770.2121398X-RAY DIFFRACTION100
3.118-3.3040.233670.2031361X-RAY DIFFRACTION100
3.304-3.5280.272650.1941227X-RAY DIFFRACTION100
3.528-3.8050.175510.1731164X-RAY DIFFRACTION100
3.805-4.1590.189490.1631105X-RAY DIFFRACTION99.7407
4.159-4.6340.194530.154982X-RAY DIFFRACTION100
4.634-5.3220.197470.151869X-RAY DIFFRACTION100
5.322-6.450.287360.191754X-RAY DIFFRACTION100
6.45-8.8470.171520.153578X-RAY DIFFRACTION100
8.847-25.680.102110.17380X-RAY DIFFRACTION99.4911

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