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- PDB-6pt5: Crystal Structure of Class D Beta-lactamase OXA-48 with Cefoxitin -

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Basic information

Entry
Database: PDB / ID: 6pt5
TitleCrystal Structure of Class D Beta-lactamase OXA-48 with Cefoxitin
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 / metal ion binding / 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-1S7 / Beta-lactamase / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.304 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 / 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
Revision 1.3Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn
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)124,85210
Polymers123,3084
Non-polymers1,5456
Water2,324129
1
A: Class D Carbapenemase OXA-48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2313
Polymers30,8271
Non-polymers4042
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)31,2313
Polymers30,8271
Non-polymers4042
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)31,1952
Polymers30,8271
Non-polymers3681
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)31,1952
Polymers30,8271
Non-polymers3681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.246, 107.115, 96.105
Angle α, β, γ (deg.)90.000, 104.060, 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.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-1S7 / (2R)-2-{(1S)-1-methoxy-2-oxo-1-[(thiophen-2-ylacetyl)amino]ethyl}-5-methylidene-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid / Cefoxitin, bound form


Mass: 368.428 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H16N2O5S2 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.44 Å3/Da / Density % sol: 49.58 %
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: 2.3→50 Å / Num. obs: 51210 / % possible obs: 97.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.04 / Rrim(I) all: 0.078 / Χ2: 0.809 / Net I/σ(I): 7.9 / Num. measured all: 187471
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.343.20.2424010.9480.1550.2870.58191.7
2.34-2.383.30.21324590.9370.1370.2550.56794.1
2.38-2.433.30.22324860.9640.140.2640.60495.7
2.43-2.483.40.20424800.9620.1290.2420.61395.6
2.48-2.533.50.18825100.9750.1170.2220.696.1
2.53-2.593.50.1825300.9760.1110.2120.61697
2.59-2.663.60.16525460.9860.1010.1940.6397.6
2.66-2.733.60.15625900.9840.0960.1830.63898.3
2.73-2.813.70.14325460.9880.0860.1670.64899
2.81-2.93.70.13925850.990.0840.1620.66199
2.9-33.80.13626010.9850.0820.1580.66799
3-3.123.80.11125760.9930.0660.1290.72798.9
3.12-3.263.90.10125770.9930.060.1170.77999.5
3.26-3.443.90.08325980.9930.0490.0970.92199.3
3.44-3.653.90.06726200.9960.040.0780.93799.4
3.65-3.933.90.05825870.9960.0340.0671.02799.3
3.93-4.333.90.04926070.9970.0290.0571.10299.4
4.33-4.953.90.04426190.9970.0260.0511.10699.7
4.95-6.243.80.04326390.9970.0260.0510.99499.7
6.24-503.70.04326530.9960.0270.0511.42598.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.46 Å27.1 Å
Translation6.46 Å27.1 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: 2.304→27.098 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 31.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2419 2022 3.96 %
Rwork0.193 49083 -
obs0.1949 51105 97.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.65 Å2 / Biso mean: 52.5514 Å2 / Biso min: 27.36 Å2
Refinement stepCycle: final / Resolution: 2.304→27.098 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7999 0 98 129 8226
Biso mean--56.27 48.25 -
Num. residues----979
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.304-2.36120.33281390.2623322590
2.3612-2.4250.34331350.2605339295
2.425-2.49630.30781470.2458344695
2.4963-2.57680.30931460.228341497
2.5768-2.66880.28541330.2184350797
2.6688-2.77560.31041450.2176349898
2.7756-2.90180.27891520.2144354799
2.9018-3.05460.31661400.2316356699
3.0546-3.24560.28951510.2165352299
3.2456-3.49580.27411350.1934358699
3.4958-3.84670.23461520.1819357699
3.8467-4.40120.22491450.1678356799
4.4012-5.53730.1621450.16433610100
5.5373-27.090.18831570.1696362799

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