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

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Basic information

Entry
Database: PDB / ID: 5eua
TitleCrystal structure of extended-spectrum beta-lactamase BEL-1 in complex with Moxalactam
ComponentsBeta-lactamase
KeywordsHYDROLASE/ANTIBIOTIC / HYDROLASE-ANTIBIOTIC complex / extended-spectrum beta-lactamase / Pseudomonas aeruginosa / oxacephem antibiotic
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
Chem-3P7 / Beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsPozzi, C. / De Luca, F. / Benvenuti, M. / 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 18, 2015Deposition site: RCSB / Processing site: PDBE
SupersessionSep 21, 2016ID: 4MXH
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 / Category: pdbx_related_exp_data_set
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7026
Polymers57,8432
Non-polymers8594
Water5,495305
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3513
Polymers28,9221
Non-polymers4292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3513
Polymers28,9221
Non-polymers4292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.530, 80.910, 86.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-lactamase /


Mass: 28921.693 Da / Num. of mol.: 2
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-3P7 / (2R)-2-[(1R)-1-{[(2R)-2-carboxy-2-(4-hydroxyphenyl)acetyl]amino}-1-methoxy-2-oxoethyl]-5-methylidene-5,6-dihydro-2H-1,3 -oxazine-4-carboxylic acid / MOXALACTAM DERIVATIVE (open form)


Mass: 406.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H18N2O9
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 305 / Source method: isolated from a natural source / Formula: H2O

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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: 2.2 Å3/Da / Density % sol: 44.21 %
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: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 5, 2013
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.85→33.58 Å / Num. obs: 42901 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Biso Wilson estimate: 19.68 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.6
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 3.8 / % possible all: 100

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Processing

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

5eoe


Resolution: 1.85→33.58 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.153 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Moxalactam in B subunit was only partially modeled due to positional disorder
RfactorNum. reflection% reflectionSelection details
Rfree0.215 2159 5 %RANDOM
Rwork0.166 ---
obs0.168 40684 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.59 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.85→33.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3888 0 53 305 4246
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.024112
X-RAY DIFFRACTIONr_bond_other_d0.0010.023871
X-RAY DIFFRACTIONr_angle_refined_deg1.6971.9935595
X-RAY DIFFRACTIONr_angle_other_deg0.8773.0028878
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1115526
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.06623.815173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.95615672
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6741532
X-RAY DIFFRACTIONr_chiral_restr0.10.2643
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214696
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02927
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_it2.1562.5972068
X-RAY DIFFRACTIONr_mcbond_other2.1522.5962067
X-RAY DIFFRACTIONr_mcangle_it3.0243.8752585
X-RAY DIFFRACTIONr_mcangle_other3.0253.8762586
X-RAY DIFFRACTIONr_scbond_it2.6162.9212044
X-RAY DIFFRACTIONr_scbond_other2.6152.9182041
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.934.2753002
X-RAY DIFFRACTIONr_long_range_B_refined5.66621.894828
X-RAY DIFFRACTIONr_long_range_B_other5.66821.8484820
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.9 Å
RfactorNum. reflection% reflection
Rfree0.267 157 -
Rwork0.229 2957 -
obs--99.94 %

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