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- PDB-7rpg: X-ray crystal structure of OXA-24/40 K84D in complex with cefotaxime -

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Basic information

Entry
Database: PDB / ID: 7rpg
TitleX-ray crystal structure of OXA-24/40 K84D in complex with cefotaxime
ComponentsBeta-lactamase
KeywordsHYDROLASE/Inhibitor / acyl-enzyme complex / carbapenemase / HYDROLASE / HYDROLASE-Inhibitor complex
Function / homologyPenicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / penicillin binding / Beta-lactamase/transpeptidase-like / beta-lactamase activity / Prokaryotic membrane lipoprotein lipid attachment site profile. / CEFOTAXIME, C3' cleaved, open, bound form / DI(HYDROXYETHYL)ETHER / Beta-lactamase
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.62 Å
AuthorsPowers, R.A. / Mitchell, J.M. / June, C.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R15AI094489-02 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI072219 United States
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Conformational flexibility in carbapenem hydrolysis drives substrate specificity of the class D carbapenemase OXA-24/40.
Authors: Mitchell, J.M. / June, C.M. / Baggett, V.L. / Lowe, B.C. / Ruble, J.F. / Bonomo, R.A. / Leonard, D.A. / Powers, R.A.
History
DepositionAug 3, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4636
Polymers27,6611
Non-polymers8025
Water5,495305
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.447, 102.447, 86.352
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-411-

HOH

21A-553-

HOH

31A-614-

HOH

41A-662-

HOH

51A-703-

HOH

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Components

#1: Protein Beta-lactamase / / Carbapenem-hydrolyzing beta-lactamase OXA-40 / Carbapenem-hydrolyzing class D beta-lactamase OXA-24 ...Carbapenem-hydrolyzing beta-lactamase OXA-40 / Carbapenem-hydrolyzing class D beta-lactamase OXA-24 / Carbapenem-hydrolyzing oxacillinase / Carbapenem-hydrolyzing oxacillinase OXA-40 / Carbapenemase OXA-24 / Class D beta-lactamase OXA-40 / OXA-24 class D beta-lactamase / OXA24 B-lactamase / Oxa40


Mass: 27660.760 Da / Num. of mol.: 1 / Mutation: K84D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: blaOXA-33, bla-OXA-40, blaOXA-24, blaOXA-40, oxa-24, oxa40, SI89_16690
Plasmid: pET24a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8RLA6, beta-lactamase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CEF / CEFOTAXIME, C3' cleaved, open, bound form / Cefotaxime


Mass: 397.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H15N5O5S2 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 305 / 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

CrystalMosaicity: 0.46 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES, 2% v/v PEG 4000, 2.0 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.62→50 Å / Num. obs: 58160 / % possible obs: 98.6 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.097 / Χ2: 1.066 / Net I/σ(I): 8.4 / Num. measured all: 448794
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.62-1.686.10.7656341.092197.2
1.68-1.757.50.68957951.0961100
1.75-1.828.10.51658121.1021100
1.82-1.928.10.3758321.0991100
1.92-2.048.10.23658491.0781100
2.04-2.28.20.14858511.0821100
2.2-2.427.40.12756901.062196.6
2.42-2.778.20.09159151.0111100
2.77-3.498.10.07959741.0181100
3.49-507.30.0558081.026192.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PAE

3pae


Resolution: 1.62→27.76 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.569 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1994 2928 5.1 %RANDOM
Rwork0.1785 ---
obs0.1795 54994 98.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 80.14 Å2 / Biso mean: 27.339 Å2 / Biso min: 12.49 Å2
Baniso -1Baniso -2Baniso -3
1--1.44 Å2-0 Å2-0 Å2
2---1.44 Å2-0 Å2
3---2.87 Å2
Refinement stepCycle: final / Resolution: 1.62→27.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1928 0 50 320 2298
Biso mean--44.28 40.73 -
Num. residues----244
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0132100
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172041
X-RAY DIFFRACTIONr_angle_refined_deg2.0051.662841
X-RAY DIFFRACTIONr_angle_other_deg1.5481.5954710
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8555263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.72823.96101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.71915394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.058159
X-RAY DIFFRACTIONr_chiral_restr0.1070.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022394
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02474
LS refinement shellResolution: 1.62→1.662 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 200 -
Rwork0.269 3920 -
all-4120 -
obs--96.49 %

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