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- PDB-1ll9: Crystal Structure Of AmpC beta-Lactamase From E. Coli In Complex ... -

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Basic information

Entry
Database: PDB / ID: 1ll9
TitleCrystal Structure Of AmpC beta-Lactamase From E. Coli In Complex With Amoxicillin
Componentsbeta-lactamase
KeywordsHYDROLASE / cephalosporinase / beta-lactamase / serine
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-AXL / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsTrehan, I. / Morandi, F. / Blaszczak, L.C. / Shoichet, B.K.
CitationJournal: Chem.Biol. / Year: 2002
Title: Using steric hindrance to design new inhibitors of class C beta-lactamases.
Authors: Trehan, I. / Morandi, F. / Blaszczak, L.C. / Shoichet, B.K.
History
DepositionApr 26, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 28, 2012Group: Other
Revision 1.4Aug 16, 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 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 600heterogen The het group AXL was origianlly amoxicillin before the compound underwent a nucleophilic ...heterogen The het group AXL was origianlly amoxicillin before the compound underwent a nucleophilic attack at the C1 by the Ser64 residue and is now covalently bound to Ser64. This attack breaks the bond between C1 and N7, thus opening the 4-membered ring.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: beta-lactamase
B: beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,5433
Polymers79,1762
Non-polymers3671
Water6,359353
1
A: beta-lactamase


Theoretical massNumber of molelcules
Total (without water)39,5881
Polymers39,5881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9552
Polymers39,5881
Non-polymers3671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.330, 76.849, 97.993
Angle α, β, γ (deg.)90, 116.505, 90
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) / Gene: ampC / Plasmid: pOGO295 / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K12 / References: UniProt: P00811, beta-lactamase
#2: Chemical ChemComp-AXL / 2-{1-[2-AMINO-2-(4-HYDROXY-PHENYL)-ACETYLAMINO]-2-OXO-ETHYL}-5,5-DIMETHYL-THIAZOLIDINE-4-CARBOXYLIC ACID / AMOXICILLIN, bound form


Mass: 367.420 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H21N3O5S / Comment: medication, antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / 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: 51.12 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: potassium phosphate, AmpC, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal grow
*PLUS
Temperature: 23 ℃ / Details: Trehan, I., (2001) Biochemistry, 40, 7992.
Components of the solutions
*PLUS
Conc.: 1.7 M / Common name: potassium phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 5, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.87→20 Å / Num. all: 63012 / Num. obs: 63012 / % possible obs: 97 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.056 / Net I/σ(I): 30.7
Reflection shellResolution: 1.87→1.91 Å / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 3.92 / % possible all: 97
Reflection
*PLUS
Lowest resolution: 20 Å / % possible obs: 97 % / Num. measured all: 225850 / Rmerge(I) obs: 0.056
Reflection shell
*PLUS
% possible obs: 97 % / Rmerge(I) obs: 0.373

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1KE4 with solvent atoms removed

1ke4


Resolution: 1.87→20 Å / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.223 2048 -random
Rwork0.1988 ---
all-56774 --
obs-56774 97 %-
Refinement stepCycle: LAST / Resolution: 1.87→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5592 0 25 353 5970
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.34069
X-RAY DIFFRACTIONc_bond_d0.005663
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.223 / Rfactor Rwork: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0057
X-RAY DIFFRACTIONc_angle_deg1.34

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