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- PDB-6tpm: Crystal structure of AmpC from E.coli with Relebactam (MK-7655) -

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Basic information

Entry
Database: PDB / ID: 6tpm
TitleCrystal structure of AmpC from E.coli with Relebactam (MK-7655)
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-MK7 / DI(HYDROXYETHYL)ETHER / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.72 Å
AuthorsLang, P.A. / Leissing, T.M. / Schofield, C.J. / Brem, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, 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
DepositionDec 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 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)40,5989
Polymers39,5881
Non-polymers1,0108
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-84 kcal/mol
Surface area13780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.500, 138.500, 138.500
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-603-

ZN

21A-608-

CL

31A-961-

HOH

41A-966-

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 (strain K12) (bacteria)
Gene: ampC, ampA, b4150, JW4111 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P00811, beta-lactamase

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Non-polymers , 7 types, 312 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-MK7 / (2S,5R)-1-formyl-N-(piperidin-4-yl)-5-[(sulfooxy)amino]piperidine-2-carboxamide / MK-7655, bound form


Mass: 350.391 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H22N4O6S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 304 / 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: 2.8 Å3/Da / Density % sol: 56.01 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 26% 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: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.72→56.54 Å / Num. obs: 48671 / % possible obs: 100 % / Redundancy: 77.1 % / CC1/2: 1 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.013 / Rrim(I) all: 0.114 / Net I/σ(I): 31.6 / Num. measured all: 3750555
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.72-1.7676.93.9771.735350.7240.4544.003100
7.69-56.5461.30.047106.966810.0060.04799.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.72 Å56.54 Å
Translation5.72 Å56.54 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.1data scaling
PHASER2.8.1phasing
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IEM

1iem


Resolution: 1.72→46.167 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.98
RfactorNum. reflection% reflection
Rfree0.1953 2443 5.03 %
Rwork0.169 --
obs0.1703 48609 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 118.56 Å2 / Biso mean: 38.5066 Å2 / Biso min: 14.66 Å2
Refinement stepCycle: final / Resolution: 1.72→46.167 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2727 0 78 313 3118
Biso mean--61.59 44.65 -
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
1.7203-1.75540.25371130.26832689
1.7554-1.79350.27441400.23632658
1.7935-1.83530.21321570.21832647
1.8353-1.88120.24811380.21122670
1.8812-1.9320.22621550.20432669
1.932-1.98890.22071440.19632679
1.9889-2.05310.21681460.18752658
2.0531-2.12650.1921550.17872670
2.1265-2.21160.17741530.17152693
2.2116-2.31220.22021530.17012680
2.3122-2.43410.19821270.16532708
2.4341-2.58660.20821240.16992736
2.5866-2.78630.19671380.17582728
2.7863-3.06670.20461530.17032741
3.0667-3.51030.18861580.17012740
3.5103-4.42210.17891230.13452830
4.4221-46.1670.18291660.17092970
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)
12.0145-0.7071-0.53699.8292-2.23632.96750.0260.0056-0.0532-0.2421-0.1277-0.13780.1093-0.1120.09340.2379-0.00390.00090.2909-0.00870.2255-3.2361-0.34216.7224
24.35382.2326-0.63435.63250.86432.84810.1423-0.3378-0.04280.2798-0.1065-0.4561-0.07410.2276-0.05870.1769-0.0105-0.00990.21490.00440.15760.53991.855417.5317
37.54581.8655-4.6190.6969-0.99273.57210.3256-0.15740.24070.2961-0.10550.0048-0.33430.1225-0.22460.3483-0.02670.00450.2682-0.04240.2216-13.15065.419628.6601
42.51680.6457-0.08752.3078-1.05252.02160.2884-0.28450.39860.538-0.07170.424-0.5719-0.2416-0.25840.487-0.0010.12890.3336-0.03550.2875-30.46948.400343.674
53.4574-0.2111-0.6594.79942.26315.6250.3292-0.3040.7330.49380.12050.1052-0.73450.0461-0.33520.51770.03590.16950.2588-0.0270.3519-27.14117.905436.1138
61.78180.1111-0.3391.8975-0.11682.40930.1846-0.06260.4220.24050.1470.113-0.7277-0.518-0.31990.44250.0840.14050.31470.01650.3125-29.057214.001330.7994
73.38920.5737-1.96081.4011-0.69352.90190.2866-0.63190.02730.3689-0.1752-0.0652-0.26410.5377-0.12690.3991-0.083-0.03650.4558-0.01440.2364-10.71141.229439.5242
83.49381.1172-1.49133.9453-0.12412.01830.0902-0.37250.31950.22940.0927-0.2011-0.25160.3887-0.17640.3033-0.0726-0.01320.3316-0.03940.2022-5.81137.659928.6378
98.5272-5.4034-0.55039.1689-0.58154.406-0.4411-0.346-0.63290.5520.20590.28520.25380.07060.23350.3189-0.06730.08470.23580.00130.2398-20.0597-10.470632.7027
108.0061-1.2149-2.93133.70053.88697.70710.09560.56330.2931-0.03510.05580.0855-0.2821-0.4949-0.1170.28590.01730.03410.28920.05150.2432-28.46131.660821.3769
112.5716-0.6408-1.71995.5305-1.79433.45490.11920.32220.3080.03010.1328-0.084-0.1155-0.3345-0.2120.25780.0559-0.0060.39870.01870.2502-24.16187.475312.3806
126.44772.0869-1.30843.1378-0.57462.6170.01140.0805-0.08370.09450.04180.0926-0.0144-0.2474-0.05210.19590.00610.00390.1610.00480.1133-21.19840.031720.7682
133.6631-0.0812-0.60525.1069-0.62993.01070.05420.1296-0.1063-0.16910.01250.2987-0.1146-0.1962-0.06790.2008-0.00330.01440.2523-0.00440.1828-12.15640.81912.5809
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 137 )A99 - 137
6X-RAY DIFFRACTION6chain 'A' and (resid 138 through 162 )A138 - 162
7X-RAY DIFFRACTION7chain 'A' and (resid 163 through 192 )A163 - 192
8X-RAY DIFFRACTION8chain 'A' and (resid 193 through 238 )A193 - 238
9X-RAY DIFFRACTION9chain 'A' and (resid 239 through 256 )A239 - 256
10X-RAY DIFFRACTION10chain 'A' and (resid 257 through 275 )A257 - 275
11X-RAY DIFFRACTION11chain 'A' and (resid 276 through 297 )A276 - 297
12X-RAY DIFFRACTION12chain 'A' and (resid 298 through 332 )A298 - 332
13X-RAY DIFFRACTION13chain 'A' and (resid 333 through 361 )A333 - 361

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