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- PDB-6tbw: Crystal structure of AmpC from E.coli with Avibactam -

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Basic information

Entry
Database: PDB / ID: 6tbw
TitleCrystal structure of AmpC from E.coli with Avibactam
ComponentsBeta-lactamase
KeywordsHYDROLASE / beta lactamase / antibiotic resistance / diazabicyclooctane / DBO
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic
Similarity search - Function
Beta-lactamase, class-C active site / Beta-lactamase class-C active site. / Beta-lactamase-related / Beta-lactamase / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Chem-NXL / TRIETHYLENE GLYCOL / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.51 Å
AuthorsLang, P.A. / Leissing, T.M. / Schofield, C.J. / Brem, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MRF-145-0004-TPG-AVISO United Kingdom
CitationJournal: Antimicrob.Agents Chemother. / Year: 2021
Title: Structural Investigations of the Inhibition of Escherichia coli AmpC beta-Lactamase by Diazabicyclooctanes.
Authors: Lang, P.A. / Leissing, T.M. / Page, M.G.P. / Schofield, C.J. / Brem, J.
History
DepositionNov 4, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)40,1726
Polymers39,5881
Non-polymers5845
Water6,918384
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area600 Å2
ΔGint-59 kcal/mol
Surface area13650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.083, 138.083, 138.083
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number212
Space group name H-MP4332
Components on special symmetry positions
IDModelComponents
11A-403-

ZN

21A-405-

CL

31A-827-

HOH

41A-853-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Beta-lactamase / / Cephalosporinase


Mass: 39587.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: ampC, ampA, b4150, JW4111
Production host: Escherichia coli str. K-12 substr. W3110 (bacteria)
References: UniProt: P00811, beta-lactamase

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Non-polymers , 5 types, 389 molecules

#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-NXL / (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide / avibactam, bound form / NXL104, bound form / Avibactam


Mass: 267.260 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H13N3O6S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic, inhibitor*YM
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 384 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.77 Å3/Da / Density % sol: 55.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 25% w/v PEG6000, 0.01 M ZnCl2, 0.1 M MES pH=6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97624 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 1.51→79.83 Å / Num. obs: 70726 / % possible obs: 100 % / Redundancy: 77.6 % / CC1/2: 1 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.013 / Rrim(I) all: 0.113 / Net I/σ(I): 29
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.51-1.5572.82.9582.651200.850.3472.979100
6.75-69.0366.90.04885.795410.0060.04899.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.68 Å79.72 Å

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Processing

Software
NameVersionClassificationNB
PHENIX1.15.2_3472refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IEM

1iem


Resolution: 1.51→79.72 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.26
RfactorNum. reflection% reflection
Rfree0.1808 3477 4.92 %
Rwork0.1584 --
obs0.1594 70643 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 77.4 Å2 / Biso mean: 28.2246 Å2 / Biso min: 12.96 Å2
Refinement stepCycle: final / Resolution: 1.51→79.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2730 0 30 389 3149
Biso mean--39.78 39.3 -
Num. residues----358
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.51-1.53050.25481410.23832638
1.5305-1.55240.23561580.21272636
1.5524-1.57560.20211430.20312646
1.5756-1.60020.23471260.19872605
1.6002-1.62640.23321340.19392678
1.6264-1.65450.18851480.1812603
1.6545-1.68460.17881370.18052666
1.6846-1.7170.16311210.17452651
1.717-1.7520.1881520.17452622
1.752-1.79010.18391230.17212673
1.7901-1.83180.19321580.1622625
1.8318-1.87760.20611360.16642692
1.8776-1.92830.19171460.17052629
1.9283-1.98510.17531130.15942677
1.9851-2.04920.19061420.16412693
2.0492-2.12240.17841350.15662675
2.1224-2.20740.16791390.14762670
2.2074-2.30790.16441290.1512701
2.3079-2.42960.15741390.14252686
2.4296-2.58180.1821270.14942732
2.5818-2.78110.17891380.15432723
2.7811-3.0610.16081440.1562727
3.061-3.5040.19581460.15642754
3.504-4.41460.15561540.13332783
4.4146-79.720.19881480.17052981
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)
13.9841-0.3478-1.85967.2016-2.53355.16710.0120.1258-0.0728-0.3687-0.1298-0.16280.1651-0.08920.10370.12670.00350.00630.1736-0.00660.1064-3.2339-0.30026.7243
24.13592.6534-0.22716.61621.24392.69650.1665-0.2291-0.00210.3067-0.1131-0.2449-0.02240.2492-0.06250.1084-0.00080.00530.1357-0.00090.10040.43021.457417.6071
37.17891.1365-4.00980.5184-0.443.34540.1196-0.20260.00360.1804-0.0687-0.0479-0.18610.1935-0.04730.2024-0.02520.00410.1308-0.02490.1112-13.00853.785229.3436
42.6883-1.8702-0.58654.89851.89051.28680.094-0.39230.26850.4630.13130.258-0.3594-0.1079-0.18290.4055-0.00030.14910.267-0.02490.2404-30.44628.26843.5332
51.1201-0.226-1.33952.15780.33822.40110.4026-0.09770.49290.32320.04360.0678-0.6795-0.2458-0.24520.39050.05650.17280.21120.00590.2934-27.827416.143533.8736
62.52730.5662-1.45731.1891-0.32741.97880.0718-0.40620.03390.281-0.0757-0.0853-0.08950.32220.01310.213-0.0284-0.01210.2039-0.00890.1248-10.24651.664432.9125
75.2667-0.2907-0.74332.57641.95356.98570.04280.63770.1655-0.11070.10470.1427-0.209-0.4788-0.13180.14770.00660.0240.21370.04430.1411-28.42761.659221.2964
82.61140.1302-1.86472.8501-1.05432.29420.12140.44560.27530.03550.04130.2527-0.16-0.4962-0.14370.16670.05140.0030.32660.04170.1798-24.26417.500812.4433
92.6975-0.0309-1.56061.0357-0.30232.4086-0.00030.2257-0.0563-0.01140.02850.08370.036-0.2477-0.01370.1262-0.0017-0.00550.1272-0.00020.108-16.83840.797116.9626
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 23 )A4 - 23
2X-RAY DIFFRACTION2chain 'A' and (resid 24 through 54 )A24 - 54
3X-RAY DIFFRACTION3chain 'A' and (resid 55 through 79 )A55 - 79
4X-RAY DIFFRACTION4chain 'A' and (resid 80 through 98 )A80 - 98
5X-RAY DIFFRACTION5chain 'A' and (resid 99 through 162 )A99 - 162
6X-RAY DIFFRACTION6chain 'A' and (resid 163 through 256 )A163 - 256
7X-RAY DIFFRACTION7chain 'A' and (resid 257 through 275 )A257 - 275
8X-RAY DIFFRACTION8chain 'A' and (resid 276 through 297 )A276 - 297
9X-RAY DIFFRACTION9chain 'A' and (resid 298 through 361 )A298 - 361

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