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- PDB-6psg: Crystal Structure of Class D Beta-lactamase OXA-48 with Faropenem -

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Basic information

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


penicillin binding / antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
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
Chem-DGF / Beta-lactamase / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.13 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 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)124,62011
Polymers123,3084
Non-polymers1,3127
Water6,161342
1
A: Class D Carbapenemase OXA-48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1503
Polymers30,8271
Non-polymers3232
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)31,1142
Polymers30,8271
Non-polymers2871
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)31,2424
Polymers30,8271
Non-polymers4153
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)31,1142
Polymers30,8271
Non-polymers2871
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.555, 106.674, 96.261
Angle α, β, γ (deg.)90.000, 104.190, 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 / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-DGF / (2R,5R)-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-5-[(2R)-tetrahydrofuran-2-yl]-2,5-dihydro-1,3-thiazole-4-carboxylic acid / FAROPENEM PRODUCT, BOUND FORM


Mass: 287.332 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H17NO5S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 2.4 Å3/Da / Density % sol: 48.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2 M Ammonium Acetate, 0.1 M Sodium Acetate pH 4.6, 30%(w/v) PEG-4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.121→50 Å / Num. obs: 64811 / % possible obs: 98.8 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.049 / Rrim(I) all: 0.092 / Χ2: 1.047 / Net I/σ(I): 6.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.13-2.172.70.36829280.920.2520.4480.65190.9
2.17-2.212.80.33331580.9450.2250.4040.66996
2.21-2.253.10.33232260.9390.2190.3990.7199
2.25-2.293.30.33732870.9370.2190.4030.70999.7
2.29-2.343.40.31832230.9630.2020.3780.69999.9
2.34-2.43.50.28232910.9640.1760.3330.72100
2.4-2.463.60.25232320.980.1570.2980.75899.8
2.46-2.533.60.22532840.9720.1390.2650.77799.8
2.53-2.63.60.19932780.9760.1230.2340.82799.7
2.6-2.683.60.1732490.9850.1050.20.83599.8
2.68-2.783.60.14832600.9860.0920.1740.93299.8
2.78-2.893.60.1332520.9870.0810.1540.98699.4
2.89-3.023.60.11432440.9910.0720.1351.01799.3
3.02-3.183.60.09332550.9910.0590.111.06398.9
3.18-3.383.60.07532340.9930.0480.091.24699.1
3.38-3.643.60.06532510.9930.0420.0771.30998.9
3.64-4.013.60.05332750.9950.0340.0631.41298.6
4.01-4.593.60.04932590.9960.0310.0581.52199
4.59-5.783.70.05232610.9950.0320.061.68899.4
5.78-503.70.05133640.9950.0320.0611.93599.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.85 Å42.75 Å
Translation6.85 Å42.75 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: 2.13→35.119 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 26.45
RfactorNum. reflection% reflection
Rfree0.2198 1994 3.08 %
Rwork0.1712 --
obs0.1727 64674 98.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 108.52 Å2 / Biso mean: 39.1952 Å2 / Biso min: 17.66 Å2
Refinement stepCycle: final / Resolution: 2.13→35.119 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8065 0 84 342 8491
Biso mean--45.02 39.86 -
Num. residues----986
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.13-2.17450.32971220.2494376283
2.1745-2.23330.29981320.2271444897
2.2333-2.2990.24351530.21254489100
2.299-2.37320.29521400.21124553100
2.3732-2.4580.28631490.20514518100
2.458-2.55630.2471490.20084550100
2.5563-2.67260.30841360.19414552100
2.6726-2.81350.25571440.18444551100
2.8135-2.98970.23821550.19452299
2.9897-3.22040.24041350.1889452199
3.2204-3.54420.24461460.1689451199
3.5442-4.05640.19351450.1518452499
4.0564-5.10810.1551440.1341453099
5.1081-35.110.17371440.14734649100

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