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- PDB-7rpb: X-ray crystal structure of OXA-24/40 V130D in complex with meropenem -

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Basic information

Entry
Database: PDB / ID: 7rpb
TitleX-ray crystal structure of OXA-24/40 V130D in complex with meropenem
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. / BICARBONATE ION / Chem-MER / Beta-lactamase
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 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)28,1984
Polymers27,6911
Non-polymers5083
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.391, 102.391, 85.647
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-465-

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: 27690.809 Da / Num. of mol.: 1 / Mutation: V130D
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-MER / (4R,5S)-3-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-4-methyl-4,5-d ihydro-1H-pyrrole-2-carboxylic acid / Meropenem, bound form / Meropenem


Mass: 385.478 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N3O5S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Chemical ChemComp-BCT / BICARBONATE ION / Bicarbonate


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 4.05 Å3/Da / Density % sol: 69.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M TRIS HCL, 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-D / Wavelength: 1.1272 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1272 Å / Relative weight: 1
ReflectionResolution: 1.97→102.391 Å / Num. obs: 29280 / % possible obs: 89.4 % / Redundancy: 7.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.054 / Rrim(I) all: 0.151 / Net I/σ(I): 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.97-1.9797.21.16921963070.6020.4611.262.292.5
9.151-102.3915.80.05720283480.9990.0220.06124.684.7

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Processing

Software
NameVersionClassification
Aimlessdata scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
AutoProcessdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PAE

3pae


Resolution: 1.97→102.39 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.566 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2292 1482 5.1 %RANDOM
Rwork0.1988 ---
obs0.2002 27753 89.47 %-
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: 118.63 Å2 / Biso mean: 46.132 Å2 / Biso min: 28.68 Å2
Baniso -1Baniso -2Baniso -3
1--1.82 Å20 Å20 Å2
2---1.82 Å20 Å2
3---3.65 Å2
Refinement stepCycle: final / Resolution: 1.97→102.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1900 0 34 70 2004
Biso mean--64.57 47.87 -
Num. residues----244
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0122012
X-RAY DIFFRACTIONr_angle_refined_deg1.9241.6542728
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6145250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.47523.71197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.26815352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9159
X-RAY DIFFRACTIONr_chiral_restr0.1230.2265
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021530
LS refinement shellResolution: 1.97→2.023 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 122 -
Rwork0.32 2179 -
all-2301 -
obs--97.17 %

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