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- PDB-7rp8: X-ray crystal structure of OXA-24/40 K84D in complex with imipenem -

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Basic information

Entry
Database: PDB / ID: 7rp8
TitleX-ray crystal structure of OXA-24/40 K84D in complex with imipenem
ComponentsBeta-lactamase
KeywordsHYDROLASE/Inhibitor / acyl-enzyme complex / carbapenemase / HYDROLASE / HYDROLASE-Inhibitor complex
Function / homology
Function and homology information


penicillin binding / beta-lactamase activity
Similarity search - Function
Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Imipenem / Beta-lactamase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.28 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
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: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3466
Polymers27,6611
Non-polymers6865
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.164, 102.164, 85.657
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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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-ID1 / Imipenem


Mass: 301.362 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N3O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 4.04 Å3/Da / Density % sol: 69.56 %
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: Feb 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.278→102.164 Å / Num. obs: 20836 / % possible obs: 97.5 % / Redundancy: 8.3 % / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.033 / Rrim(I) all: 0.097 / Net I/σ(I): 18 / Num. measured all: 171986
Reflection shellResolution: 2.278→2.285 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.617 / Num. unique obs: 209 / Rpim(I) all: 0.222 / Rrim(I) all: 0.658 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHASERphasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
AutoProcessdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JC7

2jc7


Resolution: 2.28→102.16 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.926 / SU B: 5.196 / SU ML: 0.126 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.18 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2357 1069 5.1 %RANDOM
Rwork0.1848 ---
obs0.1874 19742 97.63 %-
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: 108.95 Å2 / Biso mean: 50.131 Å2 / Biso min: 19.39 Å2
Baniso -1Baniso -2Baniso -3
1--1.71 Å20 Å20 Å2
2---1.71 Å20 Å2
3---3.42 Å2
Refinement stepCycle: final / Resolution: 2.28→102.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1902 0 40 70 2012
Biso mean--63.74 50.58 -
Num. residues----244
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0121994
X-RAY DIFFRACTIONr_angle_refined_deg1.671.642704
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6835247
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.5992495
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.58615350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.162157
X-RAY DIFFRACTIONr_chiral_restr0.1280.2262
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021490
LS refinement shellResolution: 2.28→2.337 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.304 82 -
Rwork0.242 1444 -
obs--98.83 %

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