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- PDB-9il9: Crystal Structure of SME-1 carbapenemase in complex with Avibactam. -

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Basic information

Entry
Database: PDB / ID: 9il9
TitleCrystal Structure of SME-1 carbapenemase in complex with Avibactam.
Componentsbeta-lactamase
KeywordsHYDROLASE / Carbapenemase / Complex / NXL
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase / beta-lactamase activity / 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-NXL / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Beta-lactamase SME-1
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsDhankhar, K. / Hazra, S.
Funding support India, 2items
OrganizationGrant numberCountry
Board of Research in Nuclear Sciences (BRNS)202303HLC19RP07451-BRNS India
Indian Council of Medical ResearchEM/DEV/IG/20/0773/2023 India
CitationJournal: To Be Published
Title: Crystal Structure of SME-1 carbapenemase in complex with Avibactam.
Authors: Dhankhar, K. / Hazra, S.
History
DepositionJun 29, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 2, 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)61,86910
Polymers60,8072
Non-polymers1,0638
Water3,297183
1
A: beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9436
Polymers30,4031
Non-polymers5395
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-13 kcal/mol
Surface area11100 Å2
MethodPISA
2
B: beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9274
Polymers30,4031
Non-polymers5243
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.582, 51.871, 77.429
Angle α, β, γ (deg.)90, 114.112, 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-2, blaSME-1, blaSME-4, blaSME1, SME12620_22 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q54488, beta-lactamase

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Non-polymers , 7 types, 191 molecules

#2: Chemical ChemComp-NXL / (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide / avibactam, bound form / NXL104, bound form


Mass: 267.260 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H13N3O6S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic, inhibitor*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#6: 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
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#8: 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: 2.23 Å3/Da / Density % sol: 44.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 4000, Lithium Chloride 0.2M

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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 11, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.28→24.11 Å / Num. obs: 23927 / % possible obs: 99.9 % / Redundancy: 7.6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.064 / Rrim(I) all: 0.131 / Net I/σ(I): 12.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
2.28-24.116.70.03723360.9990.0210.043
2.28-2.365.60.4324180.8690.2920.524

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Cootmodel building
CrysalisProdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→23.18 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.895 / SU B: 17.02 / SU ML: 0.18 / Cross valid method: FREE R-VALUE / ESU R Free: 0.246
RfactorNum. reflection% reflection
Rfree0.2415 1154 4.825 %
Rwork0.1548 22761 -
all0.159 --
obs-23915 99.858 %
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: 16.815 Å2
Baniso -1Baniso -2Baniso -3
1-2.076 Å20 Å2-0.595 Å2
2--0.505 Å20 Å2
3----1.462 Å2
Refinement stepCycle: LAST / Resolution: 2.28→23.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4120 0 65 183 4368
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0124290
X-RAY DIFFRACTIONr_angle_refined_deg2.7371.8245781
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8715542
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.527534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.26210758
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.1510191
X-RAY DIFFRACTIONr_chiral_restr0.1720.2632
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023230
X-RAY DIFFRACTIONr_nbd_refined0.2360.22021
X-RAY DIFFRACTIONr_nbtor_refined0.3170.22940
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2236
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2950.242
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2170.28
X-RAY DIFFRACTIONr_mcbond_it4.6841.4862150
X-RAY DIFFRACTIONr_mcangle_it7.3042.6722683
X-RAY DIFFRACTIONr_scbond_it7.6711.7022140
X-RAY DIFFRACTIONr_scangle_it10.8853.0113093
X-RAY DIFFRACTIONr_lrange_it16.52117.0716608
X-RAY DIFFRACTIONr_rigid_bond_restr7.36134290
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
2.28-2.3390.2821000.16416450.17117460.9490.98499.94270.147
2.339-2.4020.279870.17916110.18516990.9470.98199.94110.163
2.402-2.4710.277780.15715910.16216690.9540.9861000.137
2.471-2.5460.275780.18414910.18815690.9430.9811000.161
2.546-2.6280.259660.17214770.17515430.950.9831000.148
2.628-2.7190.271680.15414550.1615230.9630.9861000.131
2.719-2.8210.292670.16813800.17414470.9470.9841000.145
2.821-2.9340.272640.1813480.18414120.9390.981000.154
2.934-3.0620.275650.16812790.17313440.9490.9821000.148
3.062-3.2090.257620.15112370.15612990.960.9871000.132
3.209-3.3790.229750.15511630.15912380.9680.9891000.142
3.379-3.5790.231700.15310880.15811580.9680.9911000.144
3.579-3.820.2750.1510130.15310880.9760.9911000.14
3.82-4.1160.2320.1339960.13510280.980.9911000.117
4.116-4.4950.175270.1149360.1159640.9870.99399.89630.101
4.495-5.0020.239330.1238250.1278600.9740.99399.76740.109
5.002-5.7320.208310.1347480.1377790.9790.9921000.12
5.732-6.9150.239210.1796460.1816670.9680.9871000.164
6.915-9.3710.154290.1635050.1635340.9910.9921000.152
9.371-23.180.25260.1723250.1773520.9760.98899.71590.158

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