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- PDB-7t7g: Imipenem-OXA-23 2 minute complex -

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Basic information

Entry
Database: PDB / ID: 7t7g
TitleImipenem-OXA-23 2 minute complex
ComponentsBeta-lactamase OXA-23
KeywordsHYDROLASE / antibiotic resistance / complex
Function / homologyPenicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / penicillin binding / Beta-lactamase/transpeptidase-like / Chem-IM2 / OXA-23
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSmith, C.A. / Stewart, N.K. / Vakulenko, S.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI155723 United States
CitationJournal: Mbio / Year: 2022
Title: C6 Hydroxymethyl-Substituted Carbapenem MA-1-206 Inhibits the Major Acinetobacter baumannii Carbapenemase OXA-23 by Impeding Deacylation.
Authors: Stewart, N.K. / Toth, M. / Alqurafi, M.A. / Chai, W. / Nguyen, T.Q. / Quan, P. / Lee, M. / Buynak, J.D. / Smith, C.A. / Vakulenko, S.B.
History
DepositionDec 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase OXA-23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9912
Polymers27,6901
Non-polymers3011
Water21612
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)175.139, 175.139, 80.264
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-405-

HOH

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Components

#1: Protein Beta-lactamase OXA-23


Mass: 27689.936 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: V5TGX0
#2: Chemical ChemComp-IM2 / (5R)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-[(2-{[(E)-iminomethyl]amino}ethyl)sulfanyl]-4,5-dihydro-1H-pyrrole-2-carbox ylic acid / IMIPENEM, open form / N-FORMIMIDOYL-THIENAMYCINE, open form / 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 / Water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 5.56 Å3/Da / Density % sol: 77.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.2 M succinic acid, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.5→39.2 Å / Num. obs: 21845 / % possible obs: 100 % / Redundancy: 17 % / CC1/2: 0.999 / Rpim(I) all: 0.021 / Rrim(I) all: 0.083 / Net I/σ(I): 20.3
Reflection shellResolution: 2.5→2.6 Å / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2411 / CC1/2: 0.915 / Rpim(I) all: 0.294 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JF6

4jf6


Resolution: 2.5→39.16 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 37.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2915 1063 4.87 %
Rwork0.2568 20769 -
obs0.2586 21832 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 156.08 Å2 / Biso mean: 83.0249 Å2 / Biso min: 47.39 Å2
Refinement stepCycle: final / Resolution: 2.5→39.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1911 0 20 12 1943
Biso mean--84.19 60.45 -
Num. residues----239
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.5-2.610.34161120.356625622674
2.61-2.750.38931140.30525522666
2.75-2.920.3061340.308925702704
2.92-3.150.3891350.31725562691
3.15-3.470.26811420.271125732715
3.47-3.970.34521360.25325962732
3.97-50.23291390.217126332772
5-39.160.28391510.248327272878
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.06530.0711-0.08450.21280.19610.60490.8879-1.56881.18120.4637-0.50220.2363-0.2655-0.58710.4111.33220.1397-0.49240.7305-0.97381.845515.816862.45322.9668
21.4712-0.2087-0.59210.2951-0.4021.09810.10620.3780.26640.13220.0889-1.3134-0.16180.37270.35080.75020.1685-0.56610.7576-0.56081.900414.946655.787116.1186
33.3507-1.3881-0.54080.91570.71581.71460.0069-0.16481.5117-0.2425-0.0693-0.2415-0.162-0.22170.00630.58160.0262-0.19730.668-0.09220.82812.920942.20227.1979
40.4218-0.2942-0.30250.921-0.34080.6972-0.625-1.07930.44370.67270.5453-0.93080.37740.5018-0.00630.98390.2311-0.27490.9092-0.1360.341123.766627.472514.757
52.04280.78180.14071.9574-0.3913.56920.12310.33931.2807-0.1676-0.3319-1.0078-0.24010.09370.00040.61830.0388-0.07080.69640.10150.717816.462739.49680.325
60.3598-0.2414-0.19430.57350.34460.8333-0.0327-0.3797-0.2666-0.0042-0.2140.94970.194-0.63970.00020.6341-0.0463-0.0970.6922-0.0520.37192.455935.73087.6247
71.8961-1.0682.05653.4467-0.58232.3965-0.5274-0.77371.44530.47990.3011-0.9301-0.0434-0.0311-0.0070.81210.1735-0.25050.8289-0.30920.82814.788542.973518.1667
81.57250.87990.57731.5544-0.35513.85250.2154-0.88432.26441.10130.512-1.0681-0.0487-0.0120.23320.78440.1149-0.46370.7157-0.44451.31214.198748.405816.675
90.10030.2032-0.20760.3896-0.38570.38350.2232-1.0159-0.2790.9875-0.047-0.96480.0597-0.32530.10081.00560.379-0.62551.125-0.59371.379212.713351.509724.1893
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 35 through 46 )A35 - 46
2X-RAY DIFFRACTION2chain 'A' and (resid 47 through 57 )A47 - 57
3X-RAY DIFFRACTION3chain 'A' and (resid 58 through 101 )A58 - 101
4X-RAY DIFFRACTION4chain 'A' and (resid 102 through 127 )A102 - 127
5X-RAY DIFFRACTION5chain 'A' and (resid 128 through 185 )A128 - 185
6X-RAY DIFFRACTION6chain 'A' and (resid 186 through 202 )A186 - 202
7X-RAY DIFFRACTION7chain 'A' and (resid 203 through 225 )A203 - 225
8X-RAY DIFFRACTION8chain 'A' and (resid 226 through 255 )A226 - 255
9X-RAY DIFFRACTION9chain 'A' and (resid 256 through 273 )A256 - 273

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