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- PDB-2q9m: 4-Substituted Trinems as Broad Spectrum-Lactamase Inhibitors: Str... -

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Basic information

Entry
Database: PDB / ID: 2q9m
Title4-Substituted Trinems as Broad Spectrum-Lactamase Inhibitors: Structure-based Design, Synthesis and Biological Activity
ComponentsBeta-lactamase
KeywordsHYDROLASE / beta-lactamase inhibitor / tricyclic carbapenem
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / beta-lactamase activity / 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-LK7 / Beta-lactamase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsPlantan, I. / Selic, L. / Mesar, T. / Stefanic Anderluh, P. / Oblak, M. / Prezelj, A. / Hesse, L. / Andrejasic, M. / Vilar, M. / Turk, D. ...Plantan, I. / Selic, L. / Mesar, T. / Stefanic Anderluh, P. / Oblak, M. / Prezelj, A. / Hesse, L. / Andrejasic, M. / Vilar, M. / Turk, D. / Kocijan, A. / Prevec, T. / Vilfan, G. / Kocjan, D. / Copar, A. / Urleb, U. / Solmajer, T.
CitationJournal: J.Med.Chem. / Year: 2007
Title: 4-Substituted Trinems as Broad Spectrum beta-Lactamase Inhibitors: Structure-Based Design, Synthesis, and Biological Activity
Authors: Plantan, I. / Selic, L. / Mesar, T. / Anderluh, P.S. / Oblak, M. / Prezelj, A. / Hesse, L. / Andrejasic, M. / Vilar, M. / Turk, D. / Kocijan, A. / Prevec, T. / Vilfan, G. / Kocjan, D. / ...Authors: Plantan, I. / Selic, L. / Mesar, T. / Anderluh, P.S. / Oblak, M. / Prezelj, A. / Hesse, L. / Andrejasic, M. / Vilar, M. / Turk, D. / Kocijan, A. / Prevec, T. / Vilfan, G. / Kocjan, D. / Copar, A. / Urleb, U. / Solmajer, T.
History
DepositionJun 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
A: (1R,4S,7AS)-1-(1-FORMYLPROP-1-EN-1-YL)-4-METHOXY-2,4,5,6,7,7A-HEXAHYDRO-1H-ISOINDOLE-3-CARBOXYLIC ACID
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3062
Polymers39,0411
Non-polymers2651
Water6,630368
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.652, 69.776, 62.818
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Beta-lactamase / / Cephalosporinase


Mass: 39040.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterobacter cloacae (bacteria) / Strain: 908R / References: UniProt: P05364, beta-lactamase
#2: Chemical ChemComp-LK7 / (1R,4S,7AS)-1-(1-FORMYLPROP-1-EN-1-YL)-4-METHOXY-2,4,5,6,7,7A-HEXAHYDRO-1H-ISOINDOLE-3-CARBOXYLIC ACID


Mass: 265.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H19NO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 368 / 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: 2.15 Å3/Da / Density % sol: 42.79 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.05M Cacodylate, 30% PEG8000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 29, 2001
RadiationMonochromator: Double Crystal (Si111, Si220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. obs: 21206 / % possible obs: 96.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.05→2.09 Å / % possible all: 84.9

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Processing

Software
NameClassification
MAR345dtbdata collection
AMoREphasing
MAINrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1XX2
Resolution: 2.05→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1060 5 %random
Rwork0.209 ---
all0.209 ---
obs0.209 21206 96.8 %-
Refinement stepCycle: LAST / Resolution: 2.05→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2751 0 19 368 3138
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.0122
X-RAY DIFFRACTIONx_angle_deg1.686
LS refinement shellResolution: 2.05→2.09 Å / % reflection obs: 84.9 %

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