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- PDB-6zrg: Crystal structure of OXA-10loop48 in complex with hydrolyzed doripenem -

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Basic information

Entry
Database: PDB / ID: 6zrg
TitleCrystal structure of OXA-10loop48 in complex with hydrolyzed doripenem
ComponentsBeta-lactamase
KeywordsHYDROLASE / Beta-lactamase / OXA-10loop48 / carbapenem / doripenem
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic / metal ion binding
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/transpeptidase-like
Similarity search - Domain/homology
Chem-QP2 / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsTassone, G. / Di Pisa, F. / Benvenuti, M. / De Luca, F. / Pozzi, C. / Docquier, J.D. / Mangani, S.
CitationJournal: To Be Published
Title: Mechanistic insights into carbapenem hydrolysis by OXA-48 and the OXA10-derived hybrids OXA-10 loop24 and loop48
Authors: Tassone, G. / Di Pisa, F. / Benvenuti, M. / De Luca, F. / Pozzi, C. / Docquier, J.D. / Mangani, S.
History
DepositionJul 13, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,15712
Polymers55,1372
Non-polymers1,02010
Water9,872548
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-28 kcal/mol
Surface area19640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.563, 93.674, 126.381
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Beta-lactamase


Mass: 27568.412 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: blaoxa-10, blaOXA-10, oxa-10, BK373_28375, CQP61_30695, E4K55_27185, FORC82_p097, GII67_09965
Plasmid: pET-24 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7BNC2, beta-lactamase

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Non-polymers , 5 types, 558 molecules

#2: Chemical ChemComp-QP2 / (4R,5S)-3-{[(3S,5S)-5-({[amino(dihydroxy)methyl]amino}methyl)pyrrolidin-3-yl]sulfanyl}-5-[(1S,2R)-1-carboxy-2-hydroxypropyl]-4-methyl-4,5-dihydro-1H-pyrrole-2-carboxylic acid / hydrolyzed doripenem


Mass: 420.481 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H28N4O7S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 548 / 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: 2.67 Å3/Da / Density % sol: 53.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 2.6 - 3 M ammonium sulfate and 100 mM bicine, pH 9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 5, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.74→52.39 Å / Num. obs: 61062 / % possible obs: 99.7 % / Redundancy: 5.5 % / Biso Wilson estimate: 17.5 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.035 / Rrim(I) all: 0.082 / Net I/σ(I): 13.5
Reflection shellResolution: 1.74→1.83 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.587 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 8793 / CC1/2: 0.862 / Rpim(I) all: 0.276 / Rrim(I) all: 0.65 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QNC

3qnc


Resolution: 1.74→52.39 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.828 / SU ML: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22 3079 5 %RANDOM
Rwork0.1834 ---
obs0.1853 57904 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 77.1 Å2 / Biso mean: 25.023 Å2 / Biso min: 9.02 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refine analyzeLuzzati coordinate error obs: 0.2009 Å
Refinement stepCycle: final / Resolution: 1.74→52.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3831 0 67 559 4457
Biso mean--37.42 37.8 -
Num. residues----484
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0124073
X-RAY DIFFRACTIONr_angle_refined_deg1.6921.6415530
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.045514
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.46223.596203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.54415710
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5061518
X-RAY DIFFRACTIONr_chiral_restr0.1240.2535
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023066
LS refinement shellResolution: 1.74→1.785 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 231 -
Rwork0.283 4210 -
all-4441 -
obs--99.84 %

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