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- PDB-4e3i: Crystal structure of AmpC beta-lactamase in complex with a design... -

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Basic information

Entry
Database: PDB / ID: 4e3i
TitleCrystal structure of AmpC beta-lactamase in complex with a designed 3-carboxyl benzyl sulfonamide boronic acid inhibitor
ComponentsBeta-lactamase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / AMPC beta-lactamase / class c / hydrolase / 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-0N3 / PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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
Revision 1.3Nov 6, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1979
Polymers79,1762
Non-polymers1,0217
Water11,403633
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1465
Polymers39,5881
Non-polymers5584
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0514
Polymers39,5881
Non-polymers4633
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.460, 77.140, 97.750
Angle α, β, γ (deg.)90.000, 116.670, 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-0N3 / 3-({[(dihydroxyboranyl)methyl]sulfamoyl}methyl)benzoic acid


Mass: 273.071 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H12BNO6S
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 633 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.52 Å3/Da / Density % sol: 51.2 %
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: Jun 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 1.6→29.545 Å / Num. obs: 98113 / % possible obs: 94.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 28.396 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 14.65
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.6-1.640.541.9918465717193.4
1.64-1.690.4292.4718012696393.8
1.69-1.740.3333.217665678294.1
1.74-1.790.2534.1317430666194.5
1.79-1.850.1955.3117038648594.6
1.85-1.910.156.6516412625694.5
1.91-1.980.1119.1315796602495
1.98-2.070.08511.4915345584395.1
2.07-2.160.06614.4114536557795
2.16-2.260.05517.1213940535995
2.26-2.390.04719.0113275512195.2
2.39-2.530.04121.2512481482995.2
2.53-2.70.03723.3411753457595.8
2.7-2.920.03226.810793421795.7
2.92-3.20.02730.339925393795.2
3.2-3.580.02333.958708351194.8
3.58-4.130.02136.537823311895
4.13-5.060.019386863268396
5.06-7.160.01837.425378209296.5
7.160.01937.81223190973.8

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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: 1.6→29.545 Å / Occupancy max: 1 / Occupancy min: 0.04 / FOM work R set: 0.8795 / SU ML: 0.44 / σ(F): 1.99 / Phase error: 19.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1888 3603 3.67 %
Rwork0.1638 --
obs0.1648 98110 94.68 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.471 Å2 / ksol: 0.395 e/Å3
Displacement parametersBiso max: 77.29 Å2 / Biso mean: 25.2824 Å2 / Biso min: 9.36 Å2
Baniso -1Baniso -2Baniso -3
1-3.7673 Å20 Å23.2883 Å2
2---2.2351 Å2-0 Å2
3----1.5321 Å2
Refinement stepCycle: LAST / Resolution: 1.6→29.545 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5485 0 61 633 6179
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015888
X-RAY DIFFRACTIONf_angle_d1.3138106
X-RAY DIFFRACTIONf_chiral_restr0.09892
X-RAY DIFFRACTIONf_plane_restr0.0071038
X-RAY DIFFRACTIONf_dihedral_angle_d14.1082147
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.6210.33941470.2913526367393
1.621-1.64320.26411520.26593646379894
1.6432-1.66670.30671460.26223522366894
1.6667-1.69160.26191500.24963583373394
1.6916-1.7180.29471010.23113633373494
1.718-1.74610.22841000.21223611371194
1.7461-1.77630.20661410.19843652379395
1.7763-1.80850.23131470.18813613376095
1.8085-1.84330.21651390.18133593373295
1.8433-1.88090.17921250.18043650377595
1.8809-1.92180.1985980.16983661375995
1.9218-1.96650.1931290.16193640376995
1.9665-2.01570.20741450.16153672381795
2.0157-2.07020.1951230.15873634375795
2.0702-2.13110.20091560.1563646380295
2.1311-2.19990.19061620.1553617377995
2.1999-2.27850.19161280.15333681380995
2.2785-2.36960.19271290.15513639376895
2.3696-2.47740.18971370.1593639377695
2.4774-2.6080.21341450.1653706385196
2.608-2.77130.18291530.16963659381296
2.7713-2.9850.17991580.16853662382096
2.985-3.28510.17691510.16233672382395
3.2851-3.75960.14611330.13823645377894
3.7596-4.73360.15051730.12633722389596
4.7336-29.54990.20251350.1713583371891
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.59070.4994-0.26431.0041-0.01361.01820.0228-0.1164-0.02090.1193-0.04530.0690.2335-0.07470.01930.1692-0.03050.00280.0858-0.01670.094524.7943-7.825722.565
21.0567-0.089-0.35812.1736-0.52491.27420.01770.15980.0926-0.2693-0.0094-0.0989-0.02240.0402-0.010.1323-0.01670.00370.13410.00680.133637.85538.32777.328
31.20830.5975-0.09651.160.11431.1010.0272-0.13570.01370.1595-0.051-0.0410.11060.05040.02340.12590.0017-0.00870.09-0.0020.105430.6966-1.696122.7364
41.2623-0.26080.25731.3081-0.11731.6381-0.1783-0.1018-0.21880.01770.1541-0.17070.45910.7232-0.0310.16220.08830.00460.34280.00490.145579.0882-10.407524.056
50.96150.3433-0.191.320.20171.89570.0232-0.12680.08370.21880.0597-0.028-0.30510.2028-0.07990.1953-0.06560.00760.1681-0.02270.142764.862515.819235.1772
60.8842-0.4212-0.36991.24330.13112.0932-0.0546-0.0598-0.0506-0.02270.0688-0.0520.17420.30280.00020.0859-0.0265-0.00660.18140.00020.122870.7748-2.683225.4185
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 4:90)A4 - 90
2X-RAY DIFFRACTION2(chain A and resid 91:182)A91 - 182
3X-RAY DIFFRACTION3(chain A and resid 183:361)A183 - 361
4X-RAY DIFFRACTION4(chain B and resid 5:83)B5 - 83
5X-RAY DIFFRACTION5(chain B and resid 84:155)B84 - 155
6X-RAY DIFFRACTION6(chain B and resid 156:361)B156 - 361

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