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- PDB-7lxg: Homocitrullinated beta-lactamase OXA-48 -

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Basic information

Entry
Database: PDB / ID: 7lxg
TitleHomocitrullinated beta-lactamase OXA-48
ComponentsBeta-lactamase
KeywordsHYDROLASE / homocitrulline / OXA-48 / beta-lactamase
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / metal ion binding
Similarity search - Function
Beta-lactamase, class-D active site / Beta-lactamase class-D active site. / : / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSerrano-Negron, J.E. / King, D.T. / Vocadlo, D.J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Human Frontier Science Program (HFSP)RGP0058/2020 Canada
CitationJournal: Nat.Chem.Biol. / Year: 2022
Title: Chemoproteomic identification of CO 2 -dependent lysine carboxylation in proteins.
Authors: King, D.T. / Zhu, S. / Hardie, D.B. / Serrano-Negron, J.E. / Madden, Z. / Kolappan, S. / Vocadlo, D.J.
History
DepositionMar 3, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 6, 2022Group: Database references / Category: citation / Item: _citation.title
Revision 1.3Jul 13, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7235
Polymers64,4952
Non-polymers2283
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-39 kcal/mol
Surface area19870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.960, 143.960, 56.030
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62

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Components

#1: Protein Beta-lactamase


Mass: 32247.693 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: YHA in the sequence stands for homocitrulline (hCit), a lysine modification.
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: bla OXA-48, bla_2, bla_3, blaOXA-48, G5637_27540, GJJ01_28680, KPE71T_00045, SAMEA3649466_05396, SAMEA3673128_05462, SAMEA3729780_05587
Production host: Escherichia coli (E. coli) / References: UniProt: Q6XEC0, beta-lactamase
#2: Chemical ChemComp-SO4 / SULFATE ION


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


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


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.76 Å3/Da / Density % sol: 55.39 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop
Details: 0.2M lithium sulphate, 0.1M BIS-Tris pH 5.5, 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 28, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→47.122 Å / Num. obs: 33900 / % possible obs: 99.7 % / Redundancy: 10.1 % / CC1/2: 1 / Net I/σ(I): 25.08
Reflection shellResolution: 2.2→2.279 Å / Num. unique obs: 3340 / CC1/2: 0.941

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4S2P

4s2p


Resolution: 2.2→47.122 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2171 1707 5.04 %
Rwork0.1677 32170 -
obs0.1702 33877 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 217.52 Å2 / Biso mean: 57.9031 Å2 / Biso min: 32.35 Å2
Refinement stepCycle: final / Resolution: 2.2→47.122 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3966 0 11 233 4210
Biso mean--54.37 55.76 -
Num. residues----484
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2001-2.26480.36031550.2882261299
2.2648-2.33790.28381720.22572651100
2.3379-2.42150.26481250.2052666100
2.4215-2.51840.25021470.18772641100
2.5184-2.6330.23971530.17712659100
2.633-2.77180.27471500.17812672100
2.7718-2.94550.27891300.18762691100
2.9455-3.17280.22941310.19482665100
3.1728-3.4920.2311980.17642740100
3.492-3.99710.20941450.14952691100
3.9971-5.0350.16041440.12862707100
5.035-47.1220.19311570.16292775100

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