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- PDB-1ga0: STRUCTURE OF THE E. CLOACAE GC1 BETA-LACTAMASE WITH A CEPHALOSPOR... -

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Basic information

Entry
Database: PDB / ID: 1ga0
TitleSTRUCTURE OF THE E. CLOACAE GC1 BETA-LACTAMASE WITH A CEPHALOSPORIN SULFONE INHIBITOR
ComponentsBETA-LACTAMASE
KeywordsHYDROLASE / mixed alpha/beta / cephalosporinase / inhibition / conformational change / class C beta-lactamase
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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-DVR / Beta-lactamase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsCrichlow, G.V. / Nukaga, M. / Buynak, J.D. / Knox, J.R.
CitationJournal: Biochemistry / Year: 2001
Title: Inhibition of class C beta-lactamases: structure of a reaction intermediate with a cephem sulfone.
Authors: Crichlow, G.V. / Nukaga, M. / Doppalapudi, V.R. / Buynak, J.D. / Knox, J.R.
History
DepositionNov 28, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Aug 9, 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 13, 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: BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1024
Polymers39,6091
Non-polymers4923
Water5,675315
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.0, 69.0, 62.5
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-693-

HOH

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Components

#1: Protein 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Fragment: DVR-II-41S / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-DVR / 3-(4-CARBAMOYL-1-CARBOXY-2-METHYLSULFONYL-BUTA-1,3-DIENYLAMINO)-INDOLIZINE-2-CARBOXYLIC ACID


Mass: 377.372 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H15N3O6S
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 315 / 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: 2.09 Å3/Da / Density % sol: 41.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 6.3 mg/ml enzyme, 5.5% PEG 3350, 9 mM imidazole; over a reservoir of 24% PEG 3350. Crystal was reacted with 9 mM DVR-II-41s in 15 mM imidazole/28% PEG 3350, pH 7.0 for 3 hr. and then soaked ...Details: 6.3 mg/ml enzyme, 5.5% PEG 3350, 9 mM imidazole; over a reservoir of 24% PEG 3350. Crystal was reacted with 9 mM DVR-II-41s in 15 mM imidazole/28% PEG 3350, pH 7.0 for 3 hr. and then soaked in an identical solution for 35 min. The crystal was soaked in a cryo-protectant solution of 25% glycerol/20 mM HEPES (pH 7)/24% PEG for 2 min. prior to cryo-freezing., VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15.6 %PEG33501drop
29.1 mMimidazole1drop
324 %PEG1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.935 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 10, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.935 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 29788 / % possible obs: 66.1 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 10.8 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 7.8
Reflection shellResolution: 1.6→2.02 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.7 / Num. unique all: 7159 / % possible all: 32.2
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 94739
Reflection shell
*PLUS
% possible obs: 32.2 % / Num. unique obs: 7159 / Num. measured obs: 12241

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1GCE

1gce


Resolution: 1.6→100 Å / Isotropic thermal model: restrained, isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
Stereochemistry target values: Engh & Huber (for the protein)
Details: Intermediate assigned occupancy of 1; however, it may be less. There are six alternate side chain conformations in the protein and one alternate conformation for atom C2 and the sulfinate ...Details: Intermediate assigned occupancy of 1; however, it may be less. There are six alternate side chain conformations in the protein and one alternate conformation for atom C2 and the sulfinate atoms of the inhibitor. A bulk solvent correction was used.
RfactorNum. reflection% reflectionSelection details
Rfree0.208 1672 -random
Rwork0.181 ---
all0.183 28503 --
obs0.183 28503 100 %-
Displacement parametersBiso mean: 14.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.2 Å
Luzzati d res low-5 Å
Refinement stepCycle: LAST / Resolution: 1.6→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2783 0 33 315 3131
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.47
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 100 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 14.7 Å2
Refine LS restraints
*PLUS
Type: c_plane_restr / Dev ideal: 1

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