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- PDB-4e3k: Crystal structure of AmpC beta-lactamase in complex with a design... -

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Basic information

Entry
Database: PDB / ID: 4e3k
TitleCrystal structure of AmpC beta-lactamase in complex with a designed 4-tetrazolyl pyridine 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-0NA / PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4299 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 1.3Oct 16, 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)79,9346
Polymers79,1762
Non-polymers7584
Water12,953719
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0624
Polymers39,5881
Non-polymers4743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8722
Polymers39,5881
Non-polymers2841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.120, 76.820, 97.830
Angle α, β, γ (deg.)90.000, 116.250, 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-0NA / [({[6-(1H-tetrazol-5-yl)pyridin-3-yl]sulfonyl}amino)methyl]boronic acid


Mass: 284.060 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H9BN6O4S
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 719 / 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: 2.54 Å3/Da / Density % sol: 51.48 %
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: Apr 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 1.4299→29.578 Å / Num. obs: 139979 / % possible obs: 95.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 23.882 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 15.21
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.4299-1.470.4452.0321244980691.3
1.47-1.510.3522.99280181028097.7
1.51-1.550.2943.8827831981596.9
1.55-1.60.1865.2728962991199.7
1.6-1.650.1476.4728129956699.7
1.65-1.710.1168.1427260926799.7
1.71-1.770.09510.1926032887199
1.77-1.850.07312.825236852599.2
1.85-1.930.07414.3421234768492.3
1.93-2.020.05218.3222541774097.3
2.02-2.130.04421.7319796706194.2
2.13-2.260.03924.3118603665993.2
2.26-2.420.03426.2518638646796.4
2.42-2.610.0328.7218075616198.3
2.61-2.860.0330.5116065558496.9
2.86-3.20.02732.914712512298
3.2-3.690.02533.9711949432394.1
3.69-4.520.02235.519874346388
4.52-6.40.01935.397342259184.8
6.40.01934.22861108363.2

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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: 1.4299→29.578 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8863 / SU ML: 0.4 / σ(F): 1.99 / Phase error: 18.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1992 5339 3.82 %
Rwork0.166 --
obs0.1673 139944 96 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.686 Å2 / ksol: 0.405 e/Å3
Displacement parametersBiso max: 87.67 Å2 / Biso mean: 22.6554 Å2 / Biso min: 8.33 Å2
Baniso -1Baniso -2Baniso -3
1-2.6189 Å20 Å2-0.1115 Å2
2--1.435 Å2-0 Å2
3----4.0539 Å2
Refinement stepCycle: LAST / Resolution: 1.4299→29.578 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5492 0 48 719 6259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015808
X-RAY DIFFRACTIONf_angle_d1.3177985
X-RAY DIFFRACTIONf_chiral_restr0.087874
X-RAY DIFFRACTIONf_plane_restr0.0071029
X-RAY DIFFRACTIONf_dihedral_angle_d12.7812092
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 (%)
1.4299-1.44620.29271720.27384119429188
1.4462-1.46320.27831780.26524273445194
1.4632-1.48110.35431850.28324456464195
1.4811-1.49980.28121910.245345864777100
1.4998-1.51950.29051890.25264533472298
1.5195-1.54040.25561870.24254483467095
1.5404-1.56240.21071920.176646064798100
1.5624-1.58570.21141930.164946214814100
1.5857-1.61050.20251940.151946774871100
1.6105-1.63690.22291940.151946344828100
1.6369-1.66510.21171910.153446004791100
1.6651-1.69530.2051940.148646604854100
1.6953-1.7280.20411690.14524650481999
1.728-1.76320.17651610.135446304791100
1.7632-1.80160.17992010.13144658485999
1.8016-1.84350.18591740.13174587476199
1.8435-1.88960.19941520.14514645479799
1.8896-1.94060.24561170.21584091420886
1.9406-1.99770.20541840.15914564474898
1.9977-2.06220.21261600.15784535469597
2.0622-2.13590.20071860.16254394458094
2.1359-2.22140.18191900.15434589477998
2.2214-2.32240.2091430.17514127427088
2.3224-2.44480.17431780.15264649482799
2.4448-2.59790.20911800.15274594477498
2.5979-2.79830.17371790.16264538471797
2.7983-3.07970.1882080.16544610481898
3.0797-3.52470.17671740.15964516469096
3.5247-4.43830.16391740.14784247442190
4.4383-29.58420.23251490.1923733388278

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