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- PDB-6pt1: Crystal Structure of Class D Beta-lactamase OXA-48 with Meropenem -

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Basic information

Entry
Database: PDB / ID: 6pt1
TitleCrystal Structure of Class D Beta-lactamase OXA-48 with Meropenem
ComponentsClass D Carbapenemase OXA-48
KeywordsHYDROLASE / Carbapenemase / Carbapenem / substrate / Hydrolyzed product
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic / plasma membrane
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 / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-MER / Beta-lactamase / Beta-lactamase OXA-48
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsAkhtar, A. / Chen, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI103158 United States
CitationJournal: Acs Infect Dis. / Year: 2020
Title: Structural Basis for Substrate Specificity and Carbapenemase Activity of OXA-48 Class D beta-Lactamase.
Authors: Akhtar, A. / Pemberton, O.A. / Chen, Y.
History
DepositionJul 14, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _citation.country ..._chem_comp.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.2Oct 11, 2023Group: 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Class D Carbapenemase OXA-48
B: Class D Carbapenemase OXA-48
C: Class D Carbapenemase OXA-48
D: Class D Carbapenemase OXA-48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,24616
Polymers123,3084
Non-polymers1,93912
Water9,800544
1
A: Class D Carbapenemase OXA-48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2834
Polymers30,8271
Non-polymers4563
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Class D Carbapenemase OXA-48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2483
Polymers30,8271
Non-polymers4212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Class D Carbapenemase OXA-48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3755
Polymers30,8271
Non-polymers5484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Class D Carbapenemase OXA-48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3404
Polymers30,8271
Non-polymers5133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.797, 106.512, 95.835
Angle α, β, γ (deg.)90.000, 104.660, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Class D Carbapenemase OXA-48


Mass: 30826.881 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaOXA / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A482LRD5, UniProt: Q6XEC0*PLUS, beta-lactamase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-MER / (4R,5S)-3-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-4-methyl-4,5-d ihydro-1H-pyrrole-2-carboxylic acid / Meropenem, bound form


Mass: 385.478 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H27N3O5S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 544 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.39 Å3/Da / Density % sol: 48.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium Acetate, 0.1 M Sodium Acetate pH-4.6, 30%(w/v) PEG-4000
PH range: 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.998→50 Å / Num. obs: 78000 / % possible obs: 99.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.051 / Rrim(I) all: 0.097 / Χ2: 1.412 / Net I/σ(I): 9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.033.40.70738550.7620.4460.8381.44599.7
2.03-2.073.40.64639050.7560.4070.7651.50299.8
2.07-2.113.50.52838770.8230.3310.6251.599.7
2.11-2.153.50.50338750.8280.3160.5951.45599.6
2.15-2.23.50.41638900.9070.260.4921.45899.6
2.2-2.253.50.40838980.9090.2550.4821.51399.7
2.25-2.313.50.3939150.920.2440.4611.48899.5
2.31-2.373.50.33438440.950.2090.3951.44199.4
2.37-2.443.50.29438540.9610.1820.3461.46699.4
2.44-2.523.50.24539210.9620.1520.2891.4599.4
2.52-2.613.50.20939000.9750.1290.2461.47199.4
2.61-2.713.60.16838820.9840.1030.1981.41299.2
2.71-2.843.60.13538900.9880.0820.1581.42699.5
2.84-2.993.60.11538920.9910.070.1351.42399.6
2.99-3.173.70.08239090.9950.050.0971.41499.9
3.17-3.423.80.05439140.9970.0330.0641.362100
3.42-3.763.80.03839210.9990.0230.0441.252100
3.76-4.313.80.02939420.9990.0170.0341.097100
4.31-5.433.80.02539440.9990.0150.0291.046100
5.43-503.60.03739720.9970.0230.0441.71798.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.85 Å30.99 Å
Translation6.85 Å30.99 Å

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Processing

Software
NameVersionClassificationNB
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
PHASER2.6.0phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HBR

3hbr


Resolution: 2→30.994 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.64
RfactorNum. reflection% reflection
Rfree0.2312 1999 2.57 %
Rwork0.1869 --
obs0.1881 77883 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 97.94 Å2 / Biso mean: 35.8475 Å2 / Biso min: 13.76 Å2
Refinement stepCycle: final / Resolution: 2→30.994 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8029 0 122 544 8695
Biso mean--46.11 38.96 -
Num. residues----982
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.04780.3531290.3015510794
2.0478-2.10320.31341450.27625411100
2.1032-2.16510.30711440.25945422100
2.1651-2.23490.29471390.2295433100
2.2349-2.31480.2531470.2257543099
2.3148-2.40740.26861440.2266537699
2.4074-2.51690.26421350.2061544399
2.5169-2.64960.24811530.2019539899
2.6496-2.81550.24021410.1963543199
2.8155-3.03270.22431450.20325426100
3.0327-3.33750.21971430.18295491100
3.3375-3.81970.22371460.15965483100
3.8197-4.80960.18991460.14285485100
4.8096-30.9940.18711420.1538554899

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