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- PDB-6zrp: Crystal structure of class D Beta-lactamase OXA-48 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 6zrp
TitleCrystal structure of class D Beta-lactamase OXA-48 in complex with meropenem
Components(Beta-lactamase) x 2
KeywordsHYDROLASE / Beta-lactamase / CHDL / OXA-48 / carbapenem / meropenem / acylenzyme
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 speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsTassone, G. / De Luca, F. / Pozzi, C. / Di Pisa, F. / Benvenuti, M. / Mangani, S. / Doquier, 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. / De Luca, F. / Pozzi, C. / Di Pisa, F. / Benvenuti, M. / Mangani, S. / Doquier, J.D.
History
DepositionJul 14, 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)124,43028
Polymers121,6734
Non-polymers2,75724
Water21,6901204
1
A: Beta-lactamase
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,13913
Polymers60,8362
Non-polymers1,30311
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,29015
Polymers60,8362
Non-polymers1,45413
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.994, 125.286, 105.199
Angle α, β, γ (deg.)90.000, 77.700, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules ADBC

#1: Protein Beta-lactamase


Mass: 30439.725 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla OXA-48, blaOXA-48, KPE71T_00045 / Plasmid: pET-9a / Production host: Escherichia coli (E. coli) / References: UniProt: Q6XEC0, beta-lactamase
#2: Protein Beta-lactamase


Mass: 30396.721 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: bla OXA-48, bla_1, bla_2, bla_5, blaOXA-48, B6R99_29845, GJD56_28020, GJJ04_29145, KPE71T_00045, SAMEA3538918_02768, SAMEA3538961_03054, SAMEA3673128_05462
Plasmid: pET-9a / Production host: Escherichia coli (E. coli) / References: UniProt: Q6XEC0, beta-lactamase

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Non-polymers , 4 types, 1228 molecules

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


Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H6O2
#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.: 1204 / 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: 2.54 Å3/Da / Density % sol: 51.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10% PEG 4000, 5-8% 1-butanol, and 100 mM HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Jul 27, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.74→45.92 Å / Num. obs: 121354 / % possible obs: 99.9 % / Redundancy: 3.1 % / Biso Wilson estimate: 15.5 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.036 / Rrim(I) all: 0.065 / Net I/σ(I): 12.2
Reflection shellResolution: 1.74→1.83 Å / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 17556 / CC1/2: 0.862 / Rpim(I) all: 0.32 / Rrim(I) all: 0.557

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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: 3HBR

3hbr


Resolution: 1.74→45.92 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.365 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1868 6074 5 %RANDOM
Rwork0.157 ---
obs0.1585 115243 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.21 Å2 / Biso mean: 24.818 Å2 / Biso min: 9.73 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2--0 Å2-0 Å2
3---0.04 Å2
Refine analyzeLuzzati coordinate error obs: 0.1716 Å
Refinement stepCycle: final / Resolution: 1.74→45.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7886 0 181 1220 9287
Biso mean--34.57 38.85 -
Num. residues----970
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0128507
X-RAY DIFFRACTIONr_angle_refined_deg1.7211.6411551
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.95851046
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.23222.5492
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.419151453
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6071550
X-RAY DIFFRACTIONr_chiral_restr0.120.21101
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.026586
LS refinement shellResolution: 1.74→1.785 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 435 -
Rwork0.288 8448 -
all-8883 -
obs--99.61 %

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