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

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Basic information

Entry
Database: PDB / ID: 6zrj
TitleCrystal structure of class D Beta-lactamase OXA-48 in complex with ertapenem
Components(Beta-lactamase) x 2
KeywordsHYDROLASE / Beta-lactamase / CHDL / OXA-48 / carbapenem / ertapenem / acylenzyme
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / 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-2RG / TRIETHYLENE GLYCOL / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
E: Beta-lactamase
F: Beta-lactamase
G: Beta-lactamase
H: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,41233
Polymers243,4758
Non-polymers4,93725
Water29,4001632
1
A: Beta-lactamase
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,32413
Polymers60,8362
Non-polymers1,48711
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Beta-lactamase
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1718
Polymers60,8792
Non-polymers1,2916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Beta-lactamase
F: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8975
Polymers60,8792
Non-polymers1,0173
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Beta-lactamase
H: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0217
Polymers60,8792
Non-polymers1,1415
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.834, 162.839, 108.158
Angle α, β, γ (deg.)90.000, 90.590, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 8 molecules ACDEFGHB

#1: Protein
Beta-lactamase


Mass: 30439.725 Da / Num. of mol.: 7
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.: 1
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 , 5 types, 1657 molecules

#3: Chemical
ChemComp-2RG / (2S,3R,4S)-4-({(3S,5S)-5-[(3-carboxyphenyl)carbamoyl]pyrrolidin-3-yl}sulfanyl)-2-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid / ERTAPENEM, bound form POST-ISOMERIZED


Mass: 477.531 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C22H27N3O7S / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antibiotic*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / 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: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1632 / 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: 2.36 Å3/Da / Density % sol: 47.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10% PEG 4000, 5-8% 1-butanol, and 100mM 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: 1.94→48.51 Å / Num. obs: 157924 / % possible obs: 97.2 % / Redundancy: 3.1 % / Biso Wilson estimate: 22.5 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.055 / Rrim(I) all: 0.099 / Net I/σ(I): 10.5
Reflection shellResolution: 1.94→2.04 Å / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 22664 / CC1/2: 0.719 / Rpim(I) all: 0.385 / Rrim(I) all: 0.667

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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: 1.94→48.51 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.982 / SU ML: 0.135 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.178 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2375 8005 5.1 %RANDOM
Rwork0.1875 ---
obs0.19 149875 97.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 109.12 Å2 / Biso mean: 28.921 Å2 / Biso min: 5.28 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20 Å2
2---0 Å2-0 Å2
3----0 Å2
Refine analyzeLuzzati coordinate error obs: 0.2337 Å
Refinement stepCycle: final / Resolution: 1.94→48.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15729 0 263 1644 17636
Biso mean--46.39 37.36 -
Num. residues----1939
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01216573
X-RAY DIFFRACTIONr_angle_refined_deg1.481.63822481
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4651997
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.12522.828930
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.323152774
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5311595
X-RAY DIFFRACTIONr_chiral_restr0.1120.22138
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212844
LS refinement shellResolution: 1.94→1.99 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 585 -
Rwork0.314 10915 -
all-11500 -
obs--95.69 %

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