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- PDB-5eoo: Crystal structure of extended-spectrum beta-lactamase BEL-1 (mono... -

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Basic information

Entry
Database: PDB / ID: 5eoo
TitleCrystal structure of extended-spectrum beta-lactamase BEL-1 (monoclinic form)
ComponentsBeta-lactamase
KeywordsHYDROLASE / Extended-Spectrum Beta-Lactamase / citrate / native / 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
CITRIC ACID / ISOPROPYL ALCOHOL / TRIETHYLENE GLYCOL / Beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 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 10, 2015Deposition site: RCSB / Processing site: PDBE
SupersessionSep 21, 2016ID: 4MXG
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 / 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
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)116,88415
Polymers115,6874
Non-polymers1,19711
Water17,006944
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4536
Polymers28,9221
Non-polymers5315
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2643
Polymers28,9221
Non-polymers3422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1142
Polymers28,9221
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0534
Polymers28,9221
Non-polymers1313
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.840, 94.690, 103.680
Angle α, β, γ (deg.)90.00, 92.64, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Beta-lactamase


Mass: 28921.693 Da / Num. of mol.: 4
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 (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q3SAW3, beta-lactamase

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Non-polymers , 6 types, 955 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 944 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 47.79 % / Description: plate-shaped crystals
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 20% PEG 4600, 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: 1.48→51.78 Å / Num. all: 197506 / Num. obs: 157506 / % possible obs: 88 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Biso Wilson estimate: 12.682 Å2 / Rmerge(I) obs: 0.149 / Net I/σ(I): 4.3
Reflection shellResolution: 1.48→1.56 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.2 / % possible all: 89.7

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Processing

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

5eoe


Resolution: 1.48→51.78 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.406 / SU ML: 0.053 / SU R Cruickshank DPI: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.074 / SU Rfree Cruickshank DPI: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18665 7727 5 %RANDOM
Rwork0.16272 ---
obs0.16394 146381 87.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.975 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.157 Å
Refinement stepCycle: LAST / Resolution: 1.48→51.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7951 0 75 944 8970
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0198413
X-RAY DIFFRACTIONr_bond_other_d0.0020.028136
X-RAY DIFFRACTIONr_angle_refined_deg1.6461.98311456
X-RAY DIFFRACTIONr_angle_other_deg0.835318759
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.85151123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.84124.006362
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.199151463
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9831564
X-RAY DIFFRACTIONr_chiral_restr0.0950.21322
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029642
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021872
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_it1.0541.3974247
X-RAY DIFFRACTIONr_mcbond_other1.0521.3974246
X-RAY DIFFRACTIONr_mcangle_it1.6022.0945325
X-RAY DIFFRACTIONr_mcangle_other1.6022.0955326
X-RAY DIFFRACTIONr_scbond_it1.6791.6374166
X-RAY DIFFRACTIONr_scbond_other1.6791.6384167
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.562.3796089
X-RAY DIFFRACTIONr_long_range_B_refined4.76912.67910361
X-RAY DIFFRACTIONr_long_range_B_other4.76912.6810362
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.48→1.518 Å
RfactorNum. reflection% reflection
Rfree0.245 551 5 %
Rwork0.231 11091 -
obs--89.96 %

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