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- PDB-7t7d: MA-1-206-OXA-23 30s complex -

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Basic information

Entry
Database: PDB / ID: 7t7d
TitleMA-1-206-OXA-23 30s complex
ComponentsBeta-lactamase OXA-23
KeywordsHYDROLASE/HYDROLASE INHIBITOR / antibiotic resistance / inhibitor / complex / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


penicillin binding / cell wall organization / beta-lactamase / response to antibiotic / plasma membrane
Similarity search - Function
: / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Chem-FDX / beta-lactamase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 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 18, 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)28,0652
Polymers27,6901
Non-polymers3751
Water39622
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)173.362, 173.362, 80.981
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

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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-FDX / (2R,4S)-2-(1,3-dihydroxypropan-2-yl)-4-{[(3R,5R)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-3,4-dihydro-2H-pyrrole-5-carboxylic acid


Mass: 375.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H25N3O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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

Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / 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: BL12-2 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.65→39.14 Å / Num. obs: 18431 / % possible obs: 100 % / Redundancy: 14.7 % / CC1/2: 0.999 / Rpim(I) all: 0.021 / Rrim(I) all: 0.08 / Net I/σ(I): 20.5
Reflection shellResolution: 2.65→2.78 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2410 / CC1/2: 0.751 / Rpim(I) all: 0.542

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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: 2.65→38.76 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2532 889 4.88 %
Rwork0.2177 17316 -
obs0.2194 18205 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 175.86 Å2 / Biso mean: 88.1142 Å2 / Biso min: 51.99 Å2
Refinement stepCycle: final / Resolution: 2.65→38.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1912 0 24 22 1958
Biso mean--91.19 75.04 -
Num. residues----239
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.65-2.820.32741410.33882841298299
2.82-3.030.31541470.287228392986100
3.03-3.340.30651480.258228502998100
3.34-3.820.27511420.216828723014100
3.82-4.810.2211480.18429003048100
4.81-38.760.23781630.206630143177100
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)
10.4810.03440.21670.7439-1.54543.30530.6652-0.96910.63720.85650.5322-0.6937-0.5077-0.38940.66990.9170.1387-0.41870.923-0.8521.874214.917859.065420.3178
23.9886-0.7516-0.11561.40151.232.5739-0.0897-0.20621.11920.07810.0505-0.0422-0.1415-0.26820.00070.64840.0373-0.22360.7773-0.03010.760212.629341.86617.3468
31.8151-1.9538-0.02742.2893-0.73091.5807-0.337-0.29140.27850.73650.1984-0.75140.270.6141-0.00030.83920.1046-0.16620.83150.00340.599322.385827.661211.655
42.00540.26040.49942.68510.08282.73120.14170.39731.1534-0.2786-0.3728-0.7082-0.1360.02350.00120.71390.0395-0.06940.70740.09920.732414.929241.925-0.0144
50.47370.1585-0.12290.48120.23820.22740.2539-0.3458-0.54730.1626-0.10221.21870.5052-0.3301-0.01020.7583-0.0308-0.04470.8406-0.03670.62642.008334.78466.8392
61.2459-0.83861.32373.9036-0.07532.2088-0.3198-0.88150.92260.47320.3242-0.82610.2785-0.05540.0020.83150.1156-0.25250.8903-0.22220.906113.995141.839418.1001
71.43440.04550.20062.4388-0.52023.33690.2727-0.55821.05041.3410.4178-0.9164-0.0634-0.07540.32630.76010.0617-0.43280.7818-0.44621.286413.773547.908216.8358
80.5445-1.20670.71232.8376-1.62890.9533-0.0315-1.5666-0.4371.35960.6827-0.2188-0.0054-0.34820.23691.02720.2321-0.40661.2955-0.51631.083912.218950.920724.5229
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 35 through 57 )A35 - 57
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 101 )A58 - 101
3X-RAY DIFFRACTION3chain 'A' and (resid 102 through 138 )A102 - 138
4X-RAY DIFFRACTION4chain 'A' and (resid 139 through 186 )A139 - 186
5X-RAY DIFFRACTION5chain 'A' and (resid 187 through 201 )A187 - 201
6X-RAY DIFFRACTION6chain 'A' and (resid 202 through 225 )A202 - 225
7X-RAY DIFFRACTION7chain 'A' and (resid 226 through 255 )A226 - 255
8X-RAY DIFFRACTION8chain 'A' and (resid 256 through 273 )A256 - 273

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