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- PDB-1ll5: X-ray crystal structure of AmpC WT beta-lactamase in complex with... -

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Basic information

Entry
Database: PDB / ID: 1ll5
TitleX-ray crystal structure of AmpC WT beta-lactamase in complex with covalently bound imipenem
Componentsbeta-lactamase
KeywordsHYDROLASE / beta-lactamase / carbapenem / imipenem
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-IM2 / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBeadle, B.M. / Shoichet, B.K.
CitationJournal: ANTIMICROB.AGENTS CHEMOTHER. / Year: 2002
Title: Structural Basis for Imipenem Inhibition of Class C beta-lactamases
Authors: Beadle, B.M. / Shoichet, B.K.
History
DepositionApr 26, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 31, 2011Group: Other
Revision 1.4Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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 1.5Nov 20, 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)79,7794
Polymers79,1762
Non-polymers6032
Water4,450247
1
A: beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8892
Polymers39,5881
Non-polymers3011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8892
Polymers39,5881
Non-polymers3011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.457, 76.911, 98.009
Angle α, β, γ (deg.)90.00, 116.16, 90.00
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: K12 / Plasmid: pOGO295 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00811, beta-lactamase
#2: Chemical ChemComp-IM2 / (5R)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-[(2-{[(E)-iminomethyl]amino}ethyl)sulfanyl]-4,5-dihydro-1H-pyrrole-2-carbox ylic acid / IMIPENEM, open form / N-FORMIMIDOYL-THIENAMYCINE, open form


Mass: 301.362 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N3O4S / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.53 Å3/Da / Density % sol: 51.36 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: 1.7 M potassium phosphate; crystal was then soaked in saturated imipenem for 40 minutes, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal grow
*PLUS
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: Mar 31, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 64997 / Num. obs: 64997 / % possible obs: 88.9 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 29.1
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 0.179 / Mean I/σ(I) obs: 7.4 / % possible all: 96.4
Reflection
*PLUS
Num. measured all: 230232
Reflection shell
*PLUS
% possible obs: 96.4 % / Mean I/σ(I) obs: 7.5

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Processing

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

1ke4


Resolution: 1.8→20 Å / σ(F): 2
Details: Residues 284-290 of chain A were not seen in the electron density.
RfactorNum. reflectionSelection details
Rfree0.251 2367 Random
Rwork0.205 --
all-64997 -
obs-58744 -
Solvent computationBsol: 0.382851 Å2 / ksol: 45.6696 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.636 Å26.501 Å21.135 Å2
2--0 Å2-7.05 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5529 0 40 247 5816
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.77
X-RAY DIFFRACTIONc_bond_d0.0147
X-RAY DIFFRACTIONc_mcbond_it1.3921.5
X-RAY DIFFRACTIONc_scbond_it2.1382
X-RAY DIFFRACTIONc_mcangle_it2.0462
X-RAY DIFFRACTIONc_scangle_it3.142.5
LS refinement shellResolution: 1.8→1.86 Å
RfactorNum. reflection
Rfree0.3119 190
Rwork0.242 -
obs-4902
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5imi11a.parimi11a.top
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 4 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.015

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