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- PDB-9io7: Crystal Structure of SME-1 Carbapenemase in complex with Zidebactam -

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Basic information

Entry
Database: PDB / ID: 9io7
TitleCrystal Structure of SME-1 Carbapenemase in complex with Zidebactam
Componentsbeta-lactamase
KeywordsHYDROLASE / Complex / DBO / Class A Carbapenemase
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-C8V / Beta-lactamase SME-1
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 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 Carbapenemase in complex with ZIdebactam
Authors: Dhankhar, K. / Hazra, S.
History
DepositionJul 8, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 16, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8593
Polymers30,4031
Non-polymers4552
Water64936
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)35.884, 50.18, 60.586
Angle α, β, γ (deg.)90, 97.939, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein beta-lactamase / SME-1


Mass: 30403.297 Da / Num. of mol.: 1
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-C8V / (2S,5R)-1-formyl-N'-[(3R)-piperidine-3-carbonyl]-5-[(sulfooxy)amino]piperidine-2-carbohydrazide / OPEN FORM - Zidebactam


Mass: 393.416 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H23N5O7S / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 1.84 Å3/Da / Density % sol: 33.1 %
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 19, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.4→23.159 Å / Num. obs: 8470 / % possible obs: 99.9 % / Redundancy: 8.3 % / CC1/2: 0.997 / Net I/σ(I): 15.9
Reflection shellResolution: 2.4→2.49 Å / Num. unique obs: 872 / CC1/2: 0.972

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
CrysalisProdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→23.159 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.852 / SU B: 22.282 / SU ML: 0.23 / Cross valid method: FREE R-VALUE / ESU R Free: 0.335 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2668 418 4.945 %
Rwork0.1833 8035 -
all0.187 --
obs-8453 99.764 %
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: 20.373 Å2
Baniso -1Baniso -2Baniso -3
1--2.893 Å2-0 Å20.216 Å2
2--0.143 Å2-0 Å2
3---2.589 Å2
Refinement stepCycle: LAST / Resolution: 2.4→23.159 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2058 0 30 36 2124
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122125
X-RAY DIFFRACTIONr_angle_refined_deg1.9271.8192864
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8815266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.165519
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.48810371
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.5051093
X-RAY DIFFRACTIONr_chiral_restr0.1260.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021599
X-RAY DIFFRACTIONr_nbd_refined0.2220.2960
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21477
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.294
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.270.244
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.5080.25
X-RAY DIFFRACTIONr_mcbond_it1.3940.6571070
X-RAY DIFFRACTIONr_mcangle_it2.3511.1791334
X-RAY DIFFRACTIONr_scbond_it1.570.7161055
X-RAY DIFFRACTIONr_scangle_it2.5421.2931530
X-RAY DIFFRACTIONr_lrange_it6.5887.953247
X-RAY DIFFRACTIONr_rigid_bond_restr3.42832125
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
2.4-2.4620.245280.1935730.1966010.9650.9781000.17
2.462-2.5290.318290.1945880.26170.9430.9761000.178
2.529-2.6010.419270.2065420.2155690.950.9751000.185
2.601-2.680.262210.1925420.1955630.9620.9791000.172
2.68-2.7670.286410.1885240.1955650.9570.9791000.171
2.767-2.8620.34250.2354940.245190.910.9681000.211
2.862-2.9690.253270.2124990.2145260.9620.971000.192
2.969-3.0880.389250.2114610.2194860.9090.971000.191
3.088-3.2220.272270.2014580.2054850.9610.9721000.194
3.222-3.3760.247250.2014260.2034510.950.9751000.197
3.376-3.5550.257200.1864230.1894430.9550.981000.184
3.555-3.7650.222200.1883810.194050.9590.97999.01230.185
3.765-4.0170.255200.1763710.183910.9620.9831000.18
4.017-4.3280.156170.1263470.1273660.9840.9999.45360.126
4.328-4.7250.107130.1213240.1213370.9910.991000.125
4.725-5.2550.255120.1462980.153110.9680.98899.67850.152
5.255-6.0170.406130.2022670.2122800.9560.9751000.207
6.017-7.2480.242150.2062150.2082310.9740.97699.56710.208
7.248-9.7820.32760.1631820.1661880.9230.9841000.171
9.782-23.1590.25270.1631200.1671270.9810.9871000.171
Refinement TLS params.Method: refined / Origin x: 12.7387 Å / Origin y: -0.1451 Å / Origin z: 14.6964 Å
111213212223313233
T0.1066 Å20.0151 Å20.0265 Å2-0.0534 Å20.0107 Å2--0.0078 Å2
L2.7863 °20.6425 °20.3419 °2-1.5928 °20.0859 °2--1.2539 °2
S0.024 Å °0.0339 Å °0.0339 Å °-0.0202 Å °-0.0206 Å °-0.0004 Å °-0.0249 Å °0.0798 Å °-0.0035 Å °
Refinement TLS groupSelection: ALL

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