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- PDB-7t7f: MA-1-206-OXA-23 25 minute complex -

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Basic information

Entry
Database: PDB / ID: 7t7f
TitleMA-1-206-OXA-23 25 minute complex
ComponentsBeta-lactamase OXA-23
KeywordsHYDROLASE/HYDROLASE INHIBITOR / antibiotic resistance / inhibitor / complex / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homologyPenicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / penicillin binding / cell wall organization / Beta-lactamase/transpeptidase-like / Chem-FDX / OXA-23
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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
Water21612
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)174.457, 174.457, 80.016
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.: 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: 5.5 Å3/Da / Density % sol: 77.62 %
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: BL12-2 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.3→39.01 Å / Num. obs: 27628 / % possible obs: 99.5 % / Redundancy: 14.9 % / CC1/2: 0.999 / Rpim(I) all: 0.02 / Rrim(I) all: 0.076 / Net I/σ(I): 18.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 15.2 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2636 / CC1/2: 0.91 / Rpim(I) all: 0.428 / % possible all: 99.1

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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: 2.3→39.01 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 36.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2728 1360 4.94 %
Rwork0.2429 26198 -
obs0.2443 27558 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 155.46 Å2 / Biso mean: 82.4729 Å2 / Biso min: 49.29 Å2
Refinement stepCycle: final / Resolution: 2.3→39.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1911 0 24 12 1947
Biso mean--78.92 64.44 -
Num. residues----239
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.380.38981240.39942543266798
2.38-2.480.39631280.349625772705100
2.48-2.590.40481460.352825932739100
2.59-2.730.36721340.31212581271599
2.73-2.90.30281390.288925662705100
2.9-3.120.32471500.288326122762100
3.12-3.440.34791410.263526192760100
3.44-3.930.24281350.228226362771100
3.93-4.950.21111350.196926652800100
4.95-39.010.24711280.222328062934100
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)
10.78190.1103-0.08231.0353-1.522.23370.0188-1.30341.08341.24370.9373-0.0692-0.4315-0.75360.23971.22350.0704-0.39491.0119-0.74931.646716.286761.464623.1671
20.97910.6752-1.09420.9748-1.55543.1407-0.70310.03540.6355-0.14490.7958-0.822-0.3067-0.5611-0.00440.76150.1746-0.36390.8845-0.37721.51789.674656.407913.7908
31.8424-1.5993-0.19251.36650.3951.81330.0867-0.21141.44720.12720.0616-0.8238-0.3239-0.26240.00010.64670.0429-0.15390.7593-0.09950.912115.872844.83776.1741
41.6966-1.4988-1.39912.37180.07032.4696-0.596-0.45290.160.50820.3041-0.37890.20570.1060.00020.87310.0707-0.21170.66090.00320.474520.998825.033710.5099
52.1497-1.0141-0.31832.70550.01072.6033-0.2396-0.11330.61320.21850.0523-0.21490.14020.1202-0.00070.61060.042-0.05390.71240.02640.457117.310931.43394.4814
61.99931.06151.081.63460.25323.47930.07780.54671.2417-0.1661-0.4212-1.0473-0.2964-0.23470.00010.65010.0196-0.07520.70740.12390.846916.335243.70151.6129
70.4070.1213-0.25040.76070.50360.6261-0.0737-0.34760.21110.1329-0.2460.52150.1385-0.813-0.00060.6732-0.0334-0.03780.9-0.04270.55662.413535.54617.5603
80.5535-0.12160.57342.0976-0.32060.7012-0.3133-0.75591.26320.75780.48070.06180.1817-0.3018-0.00050.88720.0882-0.14921.0798-0.24980.672210.112441.457620.8071
90.7668-0.12050.36784.82720.93333.9379-0.2801-0.60651.62770.51620.384-0.97420.0963-0.03290.01160.7270.0866-0.3110.7656-0.31021.152816.549447.997315.7152
102.6135-0.1241-1.39640.32470.18570.7868-0.835-1.1088-1.00110.8979-0.01580.00590.294-0.0113-0.16490.94530.2323-0.47591.0465-0.56151.075912.522451.174924.326
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 35 through 47 )A35 - 47
2X-RAY DIFFRACTION2chain 'A' and (resid 48 through 65 )A48 - 65
3X-RAY DIFFRACTION3chain 'A' and (resid 66 through 91 )A66 - 91
4X-RAY DIFFRACTION4chain 'A' and (resid 92 through 113 )A92 - 113
5X-RAY DIFFRACTION5chain 'A' and (resid 114 through 150 )A114 - 150
6X-RAY DIFFRACTION6chain 'A' and (resid 151 through 185 )A151 - 185
7X-RAY DIFFRACTION7chain 'A' and (resid 186 through 202 )A186 - 202
8X-RAY DIFFRACTION8chain 'A' and (resid 203 through 220 )A203 - 220
9X-RAY DIFFRACTION9chain 'A' and (resid 221 through 255 )A221 - 255
10X-RAY DIFFRACTION10chain 'A' and (resid 256 through 273 )A256 - 273

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