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- PDB-7rpf: X-ray crystal structure of OXA-24/40 in complex with doripenem -

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Basic information

Entry
Database: PDB / ID: 7rpf
TitleX-ray crystal structure of OXA-24/40 in complex with doripenem
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/transpeptidase-like / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Chem-4J6 / BICARBONATE ION / Chem-DRW / Beta-lactamase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 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 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

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9127
Polymers27,7181
Non-polymers1,1946
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.699, 102.699, 84.468
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-518-

HOH

21A-576-

HOH

31A-589-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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: 27717.854 Da / Num. of mol.: 1
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

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Non-polymers , 5 types, 196 molecules

#2: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3
#3: Chemical ChemComp-4J6 / (4R,5S)-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-4-methyl-3-({(3S,5S)-5-[(sulfamoylamino)methyl]pyrrolidin-3-yl}sulfanyl)-4,5-dihydro-1H-pyrrole-2-carboxylic acid / Doripenem(open form, pyrroline tautomer form 1, SP2 connection to Thio)


Mass: 422.520 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H26N4O6S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DRW / (2S,3R,4S)-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-methyl-4-({(3S,5S)-5-[(sulfamoylamino)methyl]pyrrolidin-3-yl}sulfanyl)-3,4-dihydro-2H-pyrrole-5-carboxylic acid / Doripenem(open form, pyrroline tautomer form 2, SP3 connection to Thio as S isomer)


Mass: 422.520 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H26N4O6S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.02 Å3/Da / Density % sol: 69.39 % / Mosaicity: 0.274 °
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-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 35933 / % possible obs: 99.5 % / Redundancy: 15.7 % / Rmerge(I) obs: 0.087 / Χ2: 1.073 / Net I/σ(I): 11.6 / Num. measured all: 565635
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.9-1.9713.80.38434041.023196.5
1.97-2.0514.70.2935301.097199.5
2.05-2.1415.70.22235651.12199.9
2.14-2.2516.30.19135431.1141100
2.25-2.3916.40.16235741.0851100
2.39-2.5816.40.12835851.011100
2.58-2.8416.40.10935951.0621100
2.84-3.2516.30.09836311.091100
3.25-4.0916.10.06736651.0541100
4.09-5015.20.05638411.075199.2

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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: 1.9→23.63 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.463 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.205 1865 5.2 %RANDOM
Rwork0.1718 ---
obs0.1735 34013 99.49 %-
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: 96.8 Å2 / Biso mean: 33.088 Å2 / Biso min: 16.1 Å2
Baniso -1Baniso -2Baniso -3
1--2.19 Å2-0 Å2-0 Å2
2---2.19 Å2-0 Å2
3---4.37 Å2
Refinement stepCycle: final / Resolution: 1.9→23.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1928 0 73 197 2198
Biso mean--50.71 43.04 -
Num. residues----245
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0122090
X-RAY DIFFRACTIONr_angle_refined_deg1.9741.6552842
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5295258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.47323.5100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.6615372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.585158
X-RAY DIFFRACTIONr_chiral_restr0.1420.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021576
LS refinement shellResolution: 1.902→1.951 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 138 -
Rwork0.234 2357 -
all-2495 -
obs--95.59 %

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