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- PDB-1onh: GC1 beta-lactamase with a penem inhibitor -

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Basic information

Entry
Database: PDB / ID: 1onh
TitleGC1 beta-lactamase with a penem inhibitor
Componentsclass C beta-lactamase
KeywordsHYDROLASE / MIXED ALPHA/BETA / CEPHALOSPORINASE / INHIBITION / CLASS C BETA-LACTAMASE
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-WY4 / Beta-lactamase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsNukaga, M. / Nukaga, K. / Knox, J.R.
CitationJournal: Biochemistry / Year: 2003
Title: Inhibition of Class A and Class C Beta-Lactamases by Penems: Crystallographic Structures of a Novel 1,4-Thiazepine Intermediate
Authors: Nukaga, M. / Abe, T. / Venkatesan, A.M. / Mansour, T.S. / Bonomo, R.A. / Knox, J.R.
History
DepositionFeb 27, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Aug 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_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 1.5Nov 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)40,2856
Polymers39,6091
Non-polymers6765
Water7,692427
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.288, 68.873, 62.014
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-503-

HOH

21A-504-

HOH

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Components

#1: Protein class C beta-lactamase


Mass: 39609.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: BLAC / Plasmid: PCS101 / Production host: Escherichia coli (E. coli) / Strain (production host): AS226-51 / References: UniProt: Q59401, beta-lactamase
#2: Chemical ChemComp-WY4 / 7-(5,6-DIHYDRO-8H-IMIDAZO[2,1-C][1,4]OXAZIN-2-YL)-6-FORMYL-2,7-DIHYDRO- [1,4]THIAZEPINE-3-CARBOXYLIC ACID


Mass: 307.325 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H13N3O4S
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 427 / 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: 2.17 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10% PEG 8000 in 50 mM HEPES over 20 % PEG, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
210 %PEG80001drop
350 mMHEPES1droppH7.0
420 %PEG1reservoir
5100 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9474 / 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: 1.38→50 Å / Num. obs: 65047 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 10.5
Reflection shellResolution: 1.38→1.43 Å / Redundancy: 2.52 % / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 2 / Num. unique all: 5075 / % possible all: 77
Reflection
*PLUS
Highest resolution: 1.38 Å / Num. measured all: 377696
Reflection shell
*PLUS
% possible obs: 77 % / Num. unique obs: 5075 / Num. measured obs: 12765

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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: 1.38→20 Å / Num. parameters: 30398 / Num. restraintsaints: 38104 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2017 2063 3.2 %RANDOM
Rwork0.1352 ---
all0.1383 65596 --
obs0.1383 65596 96.7 %-
Refine analyzeNum. disordered residues: 36 / Occupancy sum hydrogen: 2680.96 / Occupancy sum non hydrogen: 3219.6
Refinement stepCycle: LAST / Resolution: 1.38→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2767 0 45 427 3239
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.028
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0289
X-RAY DIFFRACTIONs_zero_chiral_vol0.06
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.069
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.015
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.003
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.053
X-RAY DIFFRACTIONs_approx_iso_adps0.094
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.202 / Rfactor Rwork: 0.138
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.029
X-RAY DIFFRACTIONs_chiral_restr0.06

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