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- PDB-6zri: Crystal structure of OXA-10loop24 in complex with meropenem -

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Basic information

Entry
Database: PDB / ID: 6zri
TitleCrystal structure of OXA-10loop24 in complex with meropenem
ComponentsBeta-lactamase
KeywordsHYDROLASE / Beta-lactamase / OXA-10loop24 / carbapenem / meropenem / acylenzyme / laboratory variant
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-DWZ / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 13, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_entity_nonpoly / struct_conn
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.2Jan 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
C: Beta-lactamase
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,79620
Polymers109,5094
Non-polymers2,28716
Water19,9791109
1
A: Beta-lactamase
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8369
Polymers54,7542
Non-polymers1,0817
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-3 kcal/mol
Surface area19240 Å2
MethodPISA
2
B: Beta-lactamase
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,96011
Polymers54,7542
Non-polymers1,2059
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-2 kcal/mol
Surface area18910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.640, 80.640, 152.290
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
Beta-lactamase


Mass: 27377.203 Da / Num. of mol.: 4
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: pLBII / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: Q7BNC2, beta-lactamase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-DWZ / (2S,3R,4S)-4-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid / Meropenem, bound form


Mass: 385.478 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H27N3O5S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1109 / 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: 2.39 Å3/Da / Density % sol: 48.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 2.6 - 3 M ammonium sulfate and 100 mM TRIS, pH 8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 1, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 1.6→63.47 Å / Num. obs: 146174 / % possible obs: 99.9 % / Redundancy: 3.1 % / Biso Wilson estimate: 12.4 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.055 / Rrim(I) all: 0.098 / Net I/σ(I): 8
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 21384 / CC1/2: 0.701 / Rpim(I) all: 0.363 / Rrim(I) all: 0.641 / % possible all: 100

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Processing

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

3qnb


Resolution: 1.6→35.66 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.855 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2071 7240 5 %RANDOM
Rwork0.1686 ---
obs0.1705 138886 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 81.34 Å2 / Biso mean: 21.039 Å2 / Biso min: 7.63 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å2-0 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.1762 Å
Refinement stepCycle: final / Resolution: 1.6→35.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7617 0 152 1126 8895
Biso mean--32.83 35.44 -
Num. residues----970
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0128251
X-RAY DIFFRACTIONr_angle_refined_deg1.91.63911236
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.85451060
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.27322.955423
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.72151407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9361539
X-RAY DIFFRACTIONr_chiral_restr0.1230.21086
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.026298
LS refinement shellResolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 596 -
Rwork0.287 10332 -
all-10928 -
obs--99.99 %

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