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- PDB-6zw2: Crystal structure of OXA-10loop48 in complex with hydrolyzed meropenem -

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Basic information

Entry
Database: PDB / ID: 6zw2
TitleCrystal structure of OXA-10loop48 in complex with hydrolyzed meropenem
ComponentsBeta-lactamase
KeywordsHYDROLASE / Beta-lactamase / OXA-10loop48 / carbapenem / meropenem
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase / beta-lactamase activity / response to antibiotic / metal ion binding / plasma membrane
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-8YL / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsTassone, G. / Di Pisa, F. / Benvenuti, M. / De Luca, F. / Pozzi, C. / Mangani, S. / Docquier, J.D.
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. / Mangani, S. / Docquier, J.D.
History
DepositionJul 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)56,67417
Polymers55,1372
Non-polymers1,53715
Water9,674537
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-27 kcal/mol
Surface area19500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.715, 93.744, 126.359
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: pET24 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7BNC2, beta-lactamase

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Non-polymers , 5 types, 552 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-8YL / (2S,3R)-2-[(2S,3R)-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-4-[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfan yl-3-methyl-2,3-dihydro-1H-pyrrole-5-carboxylic acid / Meropenem, hydrolyzed form


Mass: 401.478 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H27N3O6S
Details: Other alternative conformations for hydrolysed meropenem are not excluded in the catalytic site for the observed positional disorder.
Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 537 / 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: 2.68 Å3/Da / Density % sol: 54.16 %
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: 1.75→52.45 Å / Num. obs: 60314 / % possible obs: 99.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 16.1 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.042 / Rrim(I) all: 0.109 / Net I/σ(I): 11.5
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.713 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 8684 / CC1/2: 0.807 / Rpim(I) all: 0.31 / Rrim(I) all: 0.78 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QNC

3qnc


Resolution: 1.75→52.45 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.622 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2198 2973 4.9 %RANDOM
Rwork0.1803 ---
obs0.1822 57262 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 83.7 Å2 / Biso mean: 23.264 Å2 / Biso min: 7.71 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2---0 Å20 Å2
3----0 Å2
Refine analyzeLuzzati coordinate error obs: 0.1935 Å
Refinement stepCycle: final / Resolution: 1.75→52.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3831 0 81 553 4465
Biso mean--37.34 36.01 -
Num. residues----486
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0124082
X-RAY DIFFRACTIONr_angle_refined_deg1.6991.6375539
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9335514
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.38523.532201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.24715700
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3721518
X-RAY DIFFRACTIONr_chiral_restr0.1250.2536
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023098
LS refinement shellResolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 190 -
Rwork0.269 4200 -
all-4390 -
obs--99.43 %

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