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- PDB-6pk0: Crystal Structure of OXA-48 with Hydrolyzed Imipenem -

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Basic information

Entry
Database: PDB / ID: 6pk0
TitleCrystal Structure of OXA-48 with Hydrolyzed Imipenem
ComponentsOXA family beta-lactamase
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-HIW / Beta-lactamase / Beta-lactamase OXA-48
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 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
DepositionJun 28, 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 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: OXA family beta-lactamase
B: OXA family beta-lactamase
C: OXA family beta-lactamase
D: OXA family beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,69017
Polymers123,4804
Non-polymers2,21013
Water14,880826
1
A: OXA family beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7246
Polymers30,8701
Non-polymers8545
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: OXA family beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4645
Polymers30,8701
Non-polymers5944
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: OXA family beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3154
Polymers30,8701
Non-polymers4453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: OXA family beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1872
Polymers30,8701
Non-polymers3171
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.050, 105.430, 93.570
Angle α, β, γ (deg.)90.000, 107.960, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
OXA family beta-lactamase


Mass: 30869.881 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
#2: Chemical
ChemComp-HIW / (2R,4S)-2-[(1S,2R)-1-carboxy-2-hydroxypropyl]-4-[(2-{[(Z)-iminomethyl]amino}ethyl)sulfanyl]-3,4-dihydro-2H-pyrrole-5-ca rboxylic acid / Hydrolyzed Imipenem


Mass: 317.361 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C12H19N3O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 826 / 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: 2.21 Å3/Da / Density % sol: 44.24 %
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: 23-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→38.65 Å / Num. obs: 95960 / % possible obs: 89.5 % / Redundancy: 6.1 % / CC1/2: 0.996 / Rmerge(I) obs: 0.126 / Net I/σ(I): 11.1 / Num. measured all: 583373 / Scaling rejects: 383
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
1.75-1.785.80.9112569544510.6082.184.5
9.59-38.657.10.05346696610.99734.196.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.54 Å48.88 Å
Translation3.54 Å48.88 Å

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASER2.8.2phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HBR

3hbr


Resolution: 1.75→32.587 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2017 4846 5.05 %
Rwork0.1594 91066 -
obs0.1615 95912 89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 62.01 Å2 / Biso mean: 17.6624 Å2 / Biso min: 1.27 Å2
Refinement stepCycle: final / Resolution: 1.75→32.587 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7978 0 143 826 8947
Biso mean--25.96 25.98 -
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 (%)
1.75-1.76990.33781290.2644289784
1.7699-1.79070.30161380.2395284484
1.7907-1.81260.28521470.228286584
1.8126-1.83550.26181830.2157282485
1.8355-1.85960.26211690.2287785
1.8596-1.88510.24681320.1864289784
1.8851-1.9120.23771510.1759288585
1.912-1.94060.19541760.1744285785
1.9406-1.97090.22541610.1741287186
1.9709-2.00320.22861600.1739288684
2.0032-2.03770.24571470.1692291185
2.0377-2.07480.23311430.1712288384
2.0748-2.11470.1961660.1593284385
2.1147-2.15790.20131810.1547287585
2.1579-2.20480.1921690.1555298388
2.2048-2.2560.18721810.1564295488
2.256-2.31240.24721520.1525304388
2.3124-2.37490.21131640.1588295989
2.3749-2.44480.19791580.1524305489
2.4448-2.52370.19131610.1528304689
2.5237-2.61390.17841630.1545309591
2.6139-2.71850.18771690.1524308691
2.7185-2.84210.1851700.1499316393
2.8421-2.99190.19071660.1568321594
2.9919-3.17920.18921730.1575329896
3.1792-3.42440.20741630.1493334297
3.4244-3.76850.17361820.1472336798
3.7685-4.31280.15771540.1361340099
4.3128-5.42960.19991630.1419341798
5.4296-32.580.18111750.1605342998

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