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- PDB-6t7l: Crystal structure of AmpC from E.coli with Nacubactam (OP0595) -

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Basic information

Entry
Database: PDB / ID: 6t7l
TitleCrystal structure of AmpC from E.coli with Nacubactam (OP0595)
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-OP0 / TRIETHYLENE GLYCOL / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.47 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
DepositionOct 22, 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)40,5228
Polymers39,5881
Non-polymers9347
Water7,891438
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-71 kcal/mol
Surface area13970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.178, 138.178, 138.178
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-407-

CL

31A-789-

HOH

41A-862-

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 , 7 types, 445 molecules

#2: 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
#3: Chemical ChemComp-OP0 / (2S,5R)-N-(2-aminoethoxy)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide


Mass: 326.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H18N4O7S / 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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#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.: 438 / 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: 2.78 Å3/Da / Density % sol: 55.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 29% 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: 0.97625 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: 1.47→69.09 Å / Num. obs: 76716 / % possible obs: 100 % / Redundancy: 75.8 % / CC1/2: 1 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.015 / Rrim(I) all: 0.134 / Net I/σ(I): 25.9 / Num. measured all: 5815425 / Scaling rejects: 4318
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.47-1.5176.23.0222.355590.8310.3473.042100
6.57-69.0965.50.0589.8103110.0060.05199.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.72 Å61.8 Å
Translation5.72 Å61.8 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: 1.47→48.853 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 17.55
RfactorNum. reflection% reflection
Rfree0.1823 3720 4.87 %
Rwork0.1546 --
obs0.156 76386 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 63.47 Å2 / Biso mean: 23.4514 Å2 / Biso min: 10.16 Å2
Refinement stepCycle: final / Resolution: 1.47→48.853 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2736 0 51 461 3248
Biso mean--34.12 35.57 -
Num. residues----358
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4701-1.48870.22241320.17442639100
1.4887-1.50830.2481290.17352646100
1.5083-1.52890.20541480.17482658100
1.5289-1.55080.22741310.17642643100
1.5508-1.57390.22011140.16542676100
1.5739-1.59850.22411360.16252639100
1.5985-1.62470.21241230.15382690100
1.6247-1.65270.1911420.14442639100
1.6527-1.68280.19451330.13982668100
1.6828-1.71520.18581390.13772665100
1.7152-1.75020.19341300.14562663100
1.7502-1.78820.1921520.14012649100
1.7882-1.82980.1811420.13952664100
1.8298-1.87560.17471520.14072661100
1.8756-1.92630.20811290.1464266899
1.9263-1.9830.19181290.15252683100
1.983-2.0470.20021340.15282680100
2.047-2.12020.22121650.1562673100
2.1202-2.2050.17951300.1499267099
2.205-2.30540.16331230.1501272099
2.3054-2.42690.17581590.145266899
2.4269-2.5790.20041460.1528268999
2.579-2.77810.15981390.1545272999
2.7781-3.05760.16831540.1553270899
3.0576-3.50.1781270.16012768100
3.5-4.40910.15471270.14092818100
4.4091-48.8530.18561550.17782992100

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