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- PDB-6zrh: Crystal structure of OXA-10loop24 in complex with ertapenem -

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Basic information

Entry
Database: PDB / ID: 6zrh
TitleCrystal structure of OXA-10loop24 in complex with ertapenem
ComponentsBeta-lactamase
KeywordsHYDROLASE / Beta-lactamase / OXA-10loop24 / carbapenem / ertapenem / 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-2RG / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 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 1.1Jan 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

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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)112,28822
Polymers109,5094
Non-polymers2,77918
Water19,2941071
1
A: Beta-lactamase
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,08210
Polymers54,7542
Non-polymers1,3278
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,20612
Polymers54,7542
Non-polymers1,45210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.930, 80.930, 152.150
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-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.: 4 / Source method: obtained synthetically / Formula: C22H27N3O7S / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antibiotic*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1071 / 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: 2.4 Å3/Da / Density % sol: 48.85 %
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: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 3, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.88→35.73 Å / Num. obs: 82741 / % possible obs: 91.2 % / Redundancy: 3 % / Biso Wilson estimate: 14.7 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.076 / Rrim(I) all: 0.143 / Net I/σ(I): 6.3
Reflection shellResolution: 1.88→1.98 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 12261 / CC1/2: 0.781 / Rpim(I) all: 0.282 / Rrim(I) all: 0.538 / % possible all: 92.3

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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: 3QNB

3qnb


Resolution: 1.88→35.73 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.258 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1977 4204 5.1 %RANDOM
Rwork0.1674 ---
obs0.1689 78402 91.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 88.98 Å2 / Biso mean: 20.342 Å2 / Biso min: 7.39 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20.1 Å20 Å2
2--0.2 Å20 Å2
3----0.63 Å2
Refine analyzeLuzzati coordinate error obs: 0.1903 Å
Refinement stepCycle: final / Resolution: 1.88→35.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7643 0 156 1082 8881
Biso mean--41.84 32.57 -
Num. residues----970
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0128120
X-RAY DIFFRACTIONr_angle_refined_deg1.7441.63811003
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.11751010
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.36423.308402
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.134151387
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.131536
X-RAY DIFFRACTIONr_chiral_restr0.1170.21058
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026134
LS refinement shellResolution: 1.88→1.929 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 360 -
Rwork0.266 5828 -
all-6188 -
obs--92.08 %

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