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- PDB-1q2q: Enterobacter cloacae GC1 class C beta-lactamase complexed with pe... -

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Basic information

Entry
Database: PDB / ID: 1q2q
TitleEnterobacter cloacae GC1 class C beta-lactamase complexed with penem WAY185229
Componentsclass C beta-lactamase
KeywordsHYDROLASE / inhibition / beta-lactam antibiotics / drug design
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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-WY2 / Beta-lactamase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsNukaga, M. / Venkatesan, A.M. / Mansour, T.S. / Hujer, A. / Bonomo, R.A. / Knox, J.R.
CitationJournal: J.Med.Chem. / Year: 2004
Title: Structure-activity relationship of 6-methylidene penems bearing tricyclic heterocycles as broad-spectrum beta-lactamase inhibitors: crystallographic structures show unexpected binding of 1,4- ...Title: Structure-activity relationship of 6-methylidene penems bearing tricyclic heterocycles as broad-spectrum beta-lactamase inhibitors: crystallographic structures show unexpected binding of 1,4-thiazepine intermediates
Authors: Venkatesan, A.M. / Gu, Y. / Dos Santos, O. / Abe, T. / Agarwal, A. / Yang, Y. / Petersen, P.J. / Weiss, W.J. / Mansour, T.S. / Nukaga, M. / Hujer, A. / Bonomo, R.A. / Knox, J.R.
History
DepositionJul 25, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Aug 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
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: class C beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9643
Polymers39,5081
Non-polymers4562
Water8,143452
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.223, 69.046, 62.152
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Cell settingorthorhombic
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-945-

HOH

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Components

#1: Protein class C beta-lactamase / E.C.3.5.2.6 / beta-lactamase AmpCPIT-2


Mass: 39508.062 Da / Num. of mol.: 1 / Fragment: PENICILLINASE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: BLA / Plasmid: pHSG398 / Production host: Escherichia coli (E. coli) / Strain (production host): AS226-51 / References: UniProt: Q59401, beta-lactamase
#2: Chemical ChemComp-WY2 / (6,7-DIHYDRO-5H-CYCLOPENTA[D]IMIDAZO[2,1-B]THIAZOL-2-YL]-4,7-DIHYDRO[1,4]THIAZEPINE-3,6-DICARBOXYLIC ACID


Mass: 363.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H13N3O4S2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 452 / 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: 2.2 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG 8000, HEPES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9474 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 24, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9474 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. all: 62479 / Num. obs: 62479 / % possible obs: 96.7 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rsym value: 0.126 / Net I/σ(I): 7.7
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 5063 / Rsym value: 0.409 / % possible all: 79.6

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Processing

Software
NameClassification
SHELXL-97refinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GCE

1gce


Resolution: 1.4→20 Å / Num. parameters: 30061 / Num. restraintsaints: 37045 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.209 1861 3 %RANDOM
Rwork0.144 ---
all0.145 62428 --
obs0.145 62428 96.4 %-
Displacement parametersBiso mean: 15.4 Å2
Refine analyzeLuzzati coordinate error obs: 0.08 Å / Num. disordered residues: 19 / Occupancy sum hydrogen: 2673 / Occupancy sum non hydrogen: 3246.14
Refinement stepCycle: LAST / Resolution: 1.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2753 0 29 452 3234
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d0.026
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0285
X-RAY DIFFRACTIONs_zero_chiral_vol0.065
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.066
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.016
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.003
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.049
X-RAY DIFFRACTIONs_approx_iso_adps0.085

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