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- PDB-1rgz: Enterobacter cloacae GC1 Class C beta-Lactamase Complexed with Tr... -

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Basic information

Entry
Database: PDB / ID: 1rgz
TitleEnterobacter cloacae GC1 Class C beta-Lactamase Complexed with Transition-State Analog of Cefotaxime
Componentsclass C beta-lactamase
KeywordsHYDROLASE / cephalosporinase / enzyme inhibition / phosphonate / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-PTX / Beta-lactamase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsNukaga, M. / Kumar, S. / Nukaga, K. / Pratt, R.F. / Knox, J.R.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Hydrolysis of third-generation cephalosporins by class C beta-lactamases. Structures of a transition state analog of cefotoxamine in wild-type and extended spectrum enzymes.
Authors: Nukaga, M. / Kumar, S. / Nukaga, K. / Pratt, R.F. / Knox, J.R.
History
DepositionNov 13, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 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 1.3Aug 23, 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
Revision 1.4Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_distant_solvent_atoms / pdbx_entry_details ...pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_modification_feature / struct_conn

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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)39,9864
Polymers39,5081
Non-polymers4783
Water7,170398
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.38, 68.84, 61.99
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-507-

HOH

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Components

#1: Protein class C beta-lactamase


Mass: 39508.062 Da / Num. of mol.: 1
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: P05364, beta-lactamase
#2: Chemical ChemComp-PTX / {[(2E)-2-(2-AMINO-1,3-THIAZOL-4-YL)-2-(METHOXYIMINO)ETHANOYL]AMINO}METHYLPHOSPHONIC ACID


Mass: 294.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H11N4O5PS
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / 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: 2.06 Å3/Da / Density % sol: 40.32 %
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: 1.37→50 Å / Num. all: 64695 / Num. obs: 64695 / % possible obs: 96 % / Observed criterion σ(I): 11.1 / Redundancy: 5 % / Rsym value: 0.096 / Net I/σ(I): 11.1
Reflection shellResolution: 1.37→1.42 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 5154 / Rsym value: 0.421 / % possible all: 77.8

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Processing

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

1gce


Resolution: 1.37→20 Å / Num. parameters: 29748 / Num. restraintsaints: 37290 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The author notes that residues 219 to 225 in the omega loop, have 2 conformations (with 0.75 and 0.25 occupancies, conformers A and B respectively). Only the higher occupancy conformer (A) ...Details: The author notes that residues 219 to 225 in the omega loop, have 2 conformations (with 0.75 and 0.25 occupancies, conformers A and B respectively). Only the higher occupancy conformer (A) binds the phosphonate ligand (PTX). The preceeding residue (218) is also only linked to conformer A of residue 219. Likewise, there are two sets of water molecules in the binding site with corresponding occupancies. Therefore some waters appear to overlap with each other or with the ligand and are listed as close contacts in remark 500.
RfactorNum. reflection% reflectionSelection details
Rfree0.195 3215 5 %RANDOM
Rwork0.139 ---
all0.142 64648 --
obs0.139 64648 95.3 %-
Displacement parametersBiso mean: 17.8 Å2
Refine analyzeLuzzati coordinate error obs: 0.1 Å / Num. disordered residues: 34 / Occupancy sum hydrogen: 2675 / Occupancy sum non hydrogen: 3178.25
Refinement stepCycle: LAST / Resolution: 1.37→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2761 0 29 398 3188
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.017
X-RAY DIFFRACTIONs_angle_d0.033
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0298
X-RAY DIFFRACTIONs_zero_chiral_vol0.062
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.064
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.081
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.003
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.05
X-RAY DIFFRACTIONs_approx_iso_adps0.085

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