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- PDB-6ptu: Crystal Structure of Class D Beta-lactamase OXA-48 with Imipenem -

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Basic information

Entry
Database: PDB / ID: 6ptu
TitleCrystal Structure of Class D Beta-lactamase OXA-48 with Imipenem
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
Imipenem / Beta-lactamase / Beta-lactamase OXA-48
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.004 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 16, 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 1.3Nov 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)124,72614
Polymers123,3084
Non-polymers1,41810
Water14,484804
1
A: Class D Carbapenemase OXA-48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1994
Polymers30,8271
Non-polymers3723
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)31,1643
Polymers30,8271
Non-polymers3372
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)31,1994
Polymers30,8271
Non-polymers3723
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)31,1643
Polymers30,8271
Non-polymers3372
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.497, 106.656, 94.659
Angle α, β, γ (deg.)90.000, 107.600, 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-ID1 / Imipenem


Mass: 301.362 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H19N3O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 804 / 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: 2.28 Å3/Da / Density % sol: 46.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium Acetate, 0.1 M Sodium Acetate, 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: Dec 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 69097 / % possible obs: 93.2 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.086 / Rrim(I) all: 0.166 / Χ2: 1.422 / Net I/σ(I): 6.2 / Num. measured all: 252662
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.033.60.66432620.6390.4080.7811.31688.9
2.03-2.073.60.59232580.6540.3630.6961.50688.1
2.07-2.113.60.5232760.7420.3190.6111.38788.7
2.11-2.153.60.45532660.7550.2780.5351.34487.6
2.15-2.23.60.40832440.8180.2490.4791.35588.7
2.2-2.253.60.36832550.8390.2250.4331.52887.4
2.25-2.313.60.39832440.8270.2420.4671.43988.6
2.31-2.373.60.33832620.8750.2050.3961.32487.8
2.37-2.443.60.29832710.8990.1810.351.3588.8
2.44-2.523.60.26833360.920.1620.3141.36690.1
2.52-2.613.60.24133890.9370.1450.2821.35592.4
2.61-2.713.60.2235450.9390.1350.2591.46395.4
2.71-2.843.60.18636240.9590.1140.2191.41797.9
2.84-2.993.70.16436660.9680.0990.1921.39199.1
2.99-3.173.80.13137020.9790.0780.1521.4299.5
3.17-3.423.80.0936970.990.0540.1051.43799.3
3.42-3.763.80.0736760.9920.0410.0811.51699.4
3.76-4.313.80.05437280.9960.0320.0631.46499.4
4.31-5.433.80.04736940.9970.0280.0551.3899.4
5.43-503.70.05537020.9960.0330.0641.63597.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.58 Å33.08 Å
Translation3.58 Å33.08 Å

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Processing

Software
NameVersionClassificationNB
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HBR

3hbr


Resolution: 2.004→33.077 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2151 1995 2.89 %
Rwork0.167 67060 -
obs0.1684 69055 92.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.29 Å2 / Biso mean: 17.7988 Å2 / Biso min: 2.48 Å2
Refinement stepCycle: final / Resolution: 2.004→33.077 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7965 0 86 804 8855
Biso mean--24.5 24.85 -
Num. residues----975
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.004-2.0540.28521320.21435685
2.054-2.10950.20751300.2088456288
2.1095-2.17160.23051370.1921452388
2.1716-2.24160.27771330.1924450188
2.2416-2.32170.31431300.1996454088
2.3217-2.41470.23411370.1849453488
2.4147-2.52450.24881390.1762461090
2.5245-2.65760.18551380.1793479893
2.6576-2.8240.25431510.1742497797
2.824-3.04190.1831510.1751511899
3.0419-3.34780.2291520.1603510099
3.3478-3.83160.18311550.143515399
3.8316-4.8250.18871540.1331514899
4.825-33.0770.18021560.154514098

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