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- PDB-5eph: Crystal structure of extended-spectrum beta-lactamase BEL-1 in co... -

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Basic information

Entry
Database: PDB / ID: 5eph
TitleCrystal structure of extended-spectrum beta-lactamase BEL-1 in complex with Imipenem
ComponentsBeta-lactamase
KeywordsHYDROLASE/ANTIBIOTIC / HYDROLASE-ANTIBIOTIC complex / extended-spectrum beta-lactamase / Pseudomonas aeruginosa
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Imipenem / Beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsPozzi, C. / Benvenuti, M. / De Luca, F. / Docquier, J.D. / Mangani, S.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2016
Title: Crystal Structure of the Pseudomonas aeruginosa BEL-1 Extended-Spectrum beta-Lactamase and Its Complexes with Moxalactam and Imipenem.
Authors: Pozzi, C. / De Luca, F. / Benvenuti, M. / Poirel, L. / Nordmann, P. / Rossolini, G.M. / Mangani, S. / Docquier, J.D.
History
DepositionNov 11, 2015Deposition site: RCSB / Processing site: PDBE
SupersessionSep 21, 2016ID: 4MXB
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
Revision 1.2Dec 7, 2016Group: Database references
Revision 1.3Jan 31, 2018Group: Database references / Source and taxonomy / Category: entity_src_gen / pdbx_related_exp_data_set
Item: _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Jan 10, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,18814
Polymers115,6874
Non-polymers1,50110
Water12,340685
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2944
Polymers28,9221
Non-polymers3723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3774
Polymers28,9221
Non-polymers4553
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2593
Polymers28,9221
Non-polymers3372
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2593
Polymers28,9221
Non-polymers3372
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.980, 95.860, 103.420
Angle α, β, γ (deg.)90.00, 91.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Beta-lactamase / / extended-spectrum beta-lactamase BEL-1


Mass: 28921.693 Da / Num. of mol.: 4 / Fragment: UNP residues 19-238
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: bla(BEL1), blaBEL-1 / Plasmid: pET9a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q3SAW3, beta-lactamase
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-ID1 / Imipenem / Imipenem


Mass: 301.362 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H19N3O4S / Comment: antibiotic*YM
#4: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 685 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.46 % / Description: plate-shaped crystals
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 20% PEG4600, 20% MPD, 0.1M sodium citrate, pH 5.6 / PH range: 5.6 - 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 13, 2013
RadiationMonochromator: Si(311) and Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.79→51.68 Å / Num. obs: 91836 / % possible obs: 93.2 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Biso Wilson estimate: 16.443 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 7.5
Reflection shellResolution: 1.79→1.89 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 2.7 / % possible all: 96.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOLREPmodel building
SCALAdata scaling
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EOE

5eoe


Resolution: 1.79→51.68 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.481 / SU ML: 0.078 / SU R Cruickshank DPI: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.119 / SU Rfree Cruickshank DPI: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20239 4579 5 %RANDOM
Rwork0.1635 ---
obs0.16545 87230 92.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.741 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å2-0 Å2
3---0.01 Å2
Refine analyzeLuzzati coordinate error obs: 0.178 Å
Refinement stepCycle: LAST / Resolution: 1.79→51.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7862 0 93 685 8640
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0198131
X-RAY DIFFRACTIONr_bond_other_d0.0040.027827
X-RAY DIFFRACTIONr_angle_refined_deg1.7671.98111029
X-RAY DIFFRACTIONr_angle_other_deg0.9613.00317975
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1151049
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.84824.006342
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.442151366
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.371558
X-RAY DIFFRACTIONr_chiral_restr0.1070.21285
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0219242
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021810
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6531.9064151
X-RAY DIFFRACTIONr_mcbond_other1.6521.9064150
X-RAY DIFFRACTIONr_mcangle_it2.3192.8465182
X-RAY DIFFRACTIONr_mcangle_other2.3192.8465183
X-RAY DIFFRACTIONr_scbond_it2.2122.1693980
X-RAY DIFFRACTIONr_scbond_other2.2122.1693981
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3233.1565837
X-RAY DIFFRACTIONr_long_range_B_refined4.93216.189734
X-RAY DIFFRACTIONr_long_range_B_other4.93216.1849735
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.79→1.836 Å
RfactorNum. reflection% reflection
Rfree0.295 329 4.9 %
Rwork0.231 6692 -
obs--96.63 %

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