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- PDB-4e3l: Crystal structure of AmpC beta-lactamase in complex with a 3-chlo... -

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Basic information

Entry
Database: PDB / ID: 4e3l
TitleCrystal structure of AmpC beta-lactamase in complex with a 3-chloro-4-tetrazolyl benzene sulfonamide boronic acid inhibitor
ComponentsBeta-lactamase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / AMPC beta-lactamase / class C / cephalosporinase / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic
Similarity search - Function
Beta-lactamase, class-C active site / Beta-lactamase class-C active site. / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-0NB / PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsEidam, O. / Shoichet, B.K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Fragment-guided design of subnanomolar beta-lactamase inhibitors active in vivo.
Authors: Eidam, O. / Romagnoli, C. / Dalmasso, G. / Barelier, S. / Caselli, E. / Bonnet, R. / Shoichet, B.K. / Prati, F.
History
DepositionMar 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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)80,69811
Polymers79,1762
Non-polymers1,5229
Water10,611589
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2856
Polymers39,5881
Non-polymers6975
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4135
Polymers39,5881
Non-polymers8254
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.650, 77.220, 97.690
Angle α, β, γ (deg.)90.000, 116.420, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Beta-lactamase / Cephalosporinase


Mass: 39587.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ampA, ampC, b4150, JW4111 / Plasmid: POGO295 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00811, beta-lactamase
#2: Chemical ChemComp-0NB / [({[3-chloro-4-(1H-tetrazol-5-yl)phenyl]sulfonyl}amino)methyl]boronic acid


Mass: 317.517 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H9BClN5O4S
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 589 / 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: 2.51 Å3/Da / Density % sol: 50.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 1.7 M POTASSIUM PHOSPHATE, pH 8.8, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 1.43→29.566 Å / Num. obs: 141077 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 24.54 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 16.46
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.43-1.470.6782.07422031025196.3
1.47-1.510.5342.6412471001296.4
1.51-1.550.4023.4140184974696.8
1.55-1.60.2984.5539409953797
1.6-1.650.2345.6437934919797.2
1.65-1.710.1817.2937248901997.4
1.71-1.770.1399.2335736865297.9
1.77-1.850.10412.0234645837297.8
1.85-1.930.08114.9933113803298.2
1.93-2.020.06419.1631802772998.4
2.02-2.130.05123.230190738398.6
2.13-2.260.04426.6528362699698.8
2.26-2.420.03928.8626418654198.8
2.42-2.610.03731.124581615599.1
2.61-2.860.03433.6522313562799.2
2.86-3.20.03136.5719781514299.2
3.2-3.690.02739.517361452998.9
3.69-4.520.02441.6615078380698.5
4.52-6.40.02341.411600295697.7
6.40.02240.675253139582.3

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KE4

1ke4


Resolution: 1.43→29.566 Å / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.8981 / SU ML: 0.42 / σ(F): 1.99 / Phase error: 17.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1846 5308 3.76 %
Rwork0.1576 --
obs0.1586 141064 97.76 %
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.757 Å2 / ksol: 0.374 e/Å3
Displacement parametersBiso max: 68.88 Å2 / Biso mean: 21.1067 Å2 / Biso min: 8.96 Å2
Baniso -1Baniso -2Baniso -3
1-2.4543 Å20 Å21.4839 Å2
2---2.2827 Å2-0 Å2
3----0.1715 Å2
Refinement stepCycle: LAST / Resolution: 1.43→29.566 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5501 0 90 589 6180
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015876
X-RAY DIFFRACTIONf_angle_d1.3818083
X-RAY DIFFRACTIONf_chiral_restr0.087875
X-RAY DIFFRACTIONf_plane_restr0.0081037
X-RAY DIFFRACTIONf_dihedral_angle_d15.1082130
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.43-1.44620.29341840.25554405458996
1.4462-1.46320.30181860.2384461464796
1.4632-1.48110.25131840.23734409459396
1.4811-1.49980.27921840.21884425460997
1.4998-1.51960.2451860.21354458464497
1.5196-1.54040.25271860.19814466465297
1.5404-1.56240.22861860.18844469465597
1.5624-1.58570.19561850.16234432461797
1.5857-1.61050.20771860.15434476466297
1.6105-1.63690.20551880.15274510469897
1.6369-1.66510.19661870.14344473466098
1.6651-1.69540.18141860.14574482466898
1.6954-1.7280.1778910.14034634472598
1.728-1.76330.16941740.1374488466298
1.7633-1.80160.17551800.13254552473298
1.8016-1.84350.16771810.12924517469898
1.8435-1.88960.18351380.13144569470798
1.8896-1.94070.15051350.13794589472498
1.9407-1.99780.18321810.14154552473399
1.9978-2.06220.19431670.1484593476099
2.0622-2.13590.18571930.1524534472799
2.1359-2.22140.19151840.15064560474499
2.2214-2.32250.18581720.14674596476899
2.3225-2.44490.1931730.15174615478899
2.4449-2.5980.16491690.15724606477599
2.598-2.79840.20061910.16884590478199
2.7984-3.07970.18212100.17994609481999
3.0797-3.52480.17011690.16094634480399
3.5248-4.43840.14221980.13734626482499
4.4384-29.57210.20071740.16954426460093

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