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- PDB-4e3n: Crystal structure of AmpC beta-lactamase in complex with a 2-trif... -

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Basic information

Entry
Database: PDB / ID: 4e3n
TitleCrystal structure of AmpC beta-lactamase in complex with a 2-trifluoromethyl-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-0NE / PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 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_leaving_atom_flag / _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)80,1637
Polymers79,1762
Non-polymers9875
Water9,890549
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0343
Polymers39,5881
Non-polymers4462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1294
Polymers39,5881
Non-polymers5413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.160, 76.730, 97.900
Angle α, β, γ (deg.)90.000, 116.580, 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-0NE / [({[4-(1H-tetrazol-5-yl)-2-(trifluoromethyl)phenyl]sulfonyl}amino)methyl]boronic acid


Mass: 351.070 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H9BF3N5O4S
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 549 / 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: 50.93 %
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 / Date: Sep 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 1.49→29.574 Å / Num. obs: 127111 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.374 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 18.13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.49-1.530.6662.0536251937299.7
1.53-1.570.5162.6935715915899.8
1.57-1.620.4093.4134953891299.8
1.62-1.670.3184.3534093862799.9
1.67-1.720.2535.5633265835599.8
1.72-1.780.1947.1332522810899.8
1.78-1.850.1449.3131585786899.9
1.85-1.920.11211.6930199749799.9
1.92-2.010.08115.5229160725499.8
2.01-2.110.06319.6927712692199.9
2.11-2.220.0523.8226347657199.7
2.22-2.360.04327.4424962622599.8
2.36-2.520.03730.5223571587299.8
2.52-2.720.03334.0421913544099.7
2.72-2.980.0338.7220003502599.7
2.98-3.330.02543.7417496453399.2
3.33-3.850.0250.8616318402799.6
3.85-4.710.01853.1113748340299.4
4.71-6.660.01852.8710562264099.2
6.660.01852.614935130485.7

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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: 1.49→29.574 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8936 / SU ML: 0.37 / σ(F): 2 / Phase error: 18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1879 4760 3.74 %
Rwork0.1544 --
obs0.1557 127104 99.71 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.871 Å2 / ksol: 0.41 e/Å3
Displacement parametersBiso max: 70 Å2 / Biso mean: 21.9603 Å2 / Biso min: 9.39 Å2
Baniso -1Baniso -2Baniso -3
1-0.4978 Å20 Å24.707 Å2
2---1.9209 Å20 Å2
3---1.4231 Å2
Refinement stepCycle: LAST / Resolution: 1.49→29.574 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5513 0 61 549 6123
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115862
X-RAY DIFFRACTIONf_angle_d1.3638061
X-RAY DIFFRACTIONf_chiral_restr0.088873
X-RAY DIFFRACTIONf_plane_restr0.0081038
X-RAY DIFFRACTIONf_dihedral_angle_d15.5452137
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 (%)
1.49-1.50690.27131690.231440404209100
1.5069-1.52460.25821680.210440274195100
1.5246-1.54320.24011700.201340904260100
1.5432-1.56270.24181700.182540864256100
1.5627-1.58330.22411670.17140104177100
1.5833-1.6050.22211700.171740714241100
1.605-1.62790.22731690.165940544223100
1.6279-1.65220.22871680.153440434211100
1.6522-1.6780.21551710.152440904261100
1.678-1.70550.2151690.145440574226100
1.7055-1.7350.1989820.137141074189100
1.735-1.76650.15731590.132240994258100
1.7665-1.80050.18951650.130840754240100
1.8005-1.83720.19161630.127240544217100
1.8372-1.87720.17591400.131840994239100
1.8772-1.92080.16841090.126741494258100
1.9208-1.96880.17371530.128240824235100
1.9688-2.02210.20131500.13941074257100
2.0221-2.08150.19291660.144340574223100
2.0815-2.14870.19171700.145240644234100
2.1487-2.22550.18391540.144240824236100
2.2255-2.31460.15891480.139341184266100
2.3146-2.41990.19331590.145441134272100
2.4199-2.54740.18011690.1540704239100
2.5474-2.70690.17521470.160941174264100
2.7069-2.91570.17381740.170840554229100
2.9157-3.20880.2011820.17440904272100
3.2088-3.67240.18821440.1584104424899
3.6724-4.6240.15951860.1441014287100
4.624-29.58030.19541490.17644033418295

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