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- PDB-1l2s: X-ray crystal structure of AmpC beta-lactamase from E. coli in co... -

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Basic information

Entry
Database: PDB / ID: 1l2s
TitleX-ray crystal structure of AmpC beta-lactamase from E. coli in complex with a DOCK-predicted non-covalent inhibitor
Componentsbeta-lactamase
KeywordsHYDROLASE / beta-lactamase-inhibitor complex / cephalosporinase
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-STC / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsPowers, R.A. / Morandi, F. / Shoichet, B.K.
CitationJournal: Structure / Year: 2002
Title: Structure-based discovery of a novel, noncovalent inhibitor of AmpC beta-lactamase.
Authors: Powers, R.A. / Morandi, F. / Shoichet, B.K.
History
DepositionFeb 24, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). IN SOLUTION, AMPC IS BELIEVED TO BE FUNCTIONAL IN ITS MONOMERIC FORM.
Remark 600HETEROGEN THE CONFORMATION OF THE LIGAND STC WAS DETERMINED EXPERIMENTALLY.

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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)80,1295
Polymers79,1762
Non-polymers9533
Water6,341352
1
A: beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9062
Polymers39,5881
Non-polymers3181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2233
Polymers39,5881
Non-polymers6362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.670, 76.420, 97.900
Angle α, β, γ (deg.)90.00, 116.63, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein beta-lactamase / AMPC / 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: K12 / Plasmid: pOGO295 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00811, beta-lactamase
#2: Chemical ChemComp-STC / 3-[(4-CHLOROANILINO)SULFONYL]THIOPHENE-2-CARBOXYLIC ACID


Mass: 317.769 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H8ClNO4S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / 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: 2.5 Å3/Da / Density % sol: 50.88 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: 1.7 M potassium phosphate, 1.2 mM inhibitor (STC), pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal grow
*PLUS
Temperature: 23 ℃ / Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.7 Mpotassium phosphate1reservoirpH8.7
21.2 mMinhibitor1drop
34 %DMSO1drop
41.7 Mpotassium phosphate1droppH8.7

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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: Dec 19, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→20 Å / Num. obs: 56580 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 18.21 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 14.5
Reflection shellResolution: 1.94→1.99 Å / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 4.2 / % possible all: 95.1
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 208148 / Rmerge(I) obs: 0.055
Reflection shell
*PLUS
% possible obs: 95.1 % / Rmerge(I) obs: 0.315

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Processing

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

1ke4


Resolution: 1.94→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: Electron density for residues 290-292 of chain A was poor, and are not present in the final model.
RfactorNum. reflectionSelection details
Rfree0.207 2647 random
Rwork0.173 --
obs-52232 -
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.94→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5507 0 57 352 5916
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.88
LS refinement shellResolution: 1.94→2.03 Å
RfactorNum. reflection
Rfree0.2296 269
Rwork0.1917 -
obs-5277
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.207 / Rfactor Rwork: 0.173
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.88
LS refinement shell
*PLUS
Rfactor Rfree: 0.2296 / Rfactor Rwork: 0.1917

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