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- PDB-7t7e: MA-1-206-OXA-23 3 minute complex -

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Basic information

Entry
Database: PDB / ID: 7t7e
TitleMA-1-206-OXA-23 3 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 / Beta-lactamase/transpeptidase-like / Chem-FDX / Beta-lactamase OXA-23
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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

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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
Water30617
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)174.277, 174.277, 81.222
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 / Water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 5.57 Å3/Da / Density % sol: 77.91 %
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: Jul 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.4→39 Å / Num. obs: 24682 / % possible obs: 99.9 % / Redundancy: 8.8 % / CC1/2: 0.999 / Rpim(I) all: 0.021 / Rrim(I) all: 0.064 / Net I/σ(I): 17.4
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 8.8 % / Mean I/σ(I) obs: 2 / Num. unique obs: 2532 / CC1/2: 0.893 / Rpim(I) all: 0.318 / % possible all: 99.8

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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
Resolution: 2.4→38.97 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 32.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.26 1226 4.97 %
Rwork0.2281 23421 -
obs0.2298 24647 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 145.36 Å2 / Biso mean: 78.0539 Å2 / Biso min: 48.31 Å2
Refinement stepCycle: final / Resolution: 2.4→38.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1912 0 24 17 1953
Biso mean--77.94 70.95 -
Num. residues----239
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.4-2.50.3631300.345125462676
2.5-2.610.36141330.33225482681
2.61-2.750.30821370.288425652702
2.75-2.920.34391350.265625622697
2.92-3.140.30651250.287226022727
3.14-3.460.28651330.244525932726
3.46-3.960.25891230.225826262749
3.96-4.990.2271570.181526272784
4.99-38.970.23411530.213227522905
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.27920.2191-0.31030.3895-0.580.84960.3864-0.37990.3780.45980.0644-0.5472-0.42880.03950.08750.89370.0728-0.37180.8943-0.60031.623315.194659.179120.4569
22.5469-0.9218-0.0550.83411.09361.9104-0.0149-0.14351.17410.094-0.043-0.2455-0.1136-0.17270.00170.60340.022-0.18590.6869-0.03320.784612.81742.03817.4093
30.538-0.2361-0.30770.4575-0.28910.6691-0.4072-0.55540.18361.02580.34-0.46080.18580.1656-0.00020.84620.1149-0.17520.7621-0.04470.499123.29827.373914.8914
42.08780.7439-0.0521.92350.11142.97270.09170.12120.8497-0.1456-0.3475-0.6947-0.1989-0.0166-0.00010.59190.014-0.07160.63480.11140.632716.063339.4720.6878
51.7158-1.88261.02154.54690.04842.61-0.2159-0.48470.45250.24360.14760.02430.2095-0.3051-0.00010.60760.0425-0.08730.7431-0.08320.48869.586939.326313.7715
60.9309-0.31860.44832.2507-0.39952.69-0.3338-0.49081.60570.70650.4381-0.5929-0.1039-0.31540.0540.67080.0874-0.31510.7454-0.38071.059713.962148.099516.9757
71.0547-0.0202-0.20770.6293-0.06970.1015-0.0891-1.4239-0.43541.1790.3137-0.36750.3107-0.10130.00150.93860.2109-0.36561.1014-0.52721.08112.373351.109924.5085
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 127 )A102 - 127
4X-RAY DIFFRACTION4chain 'A' and (resid 128 through 186 )A128 - 186
5X-RAY DIFFRACTION5chain 'A' and (resid 187 through 225 )A187 - 225
6X-RAY DIFFRACTION6chain 'A' and (resid 226 through 255 )A226 - 255
7X-RAY DIFFRACTION7chain 'A' and (resid 256 through 273 )A256 - 273

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