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- PDB-4gzb: Crystal structure of native AmpC beta-lactamase from Pseudomonas ... -

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Basic information

Entry
Database: PDB / ID: 4gzb
TitleCrystal structure of native AmpC beta-lactamase from Pseudomonas aeruginosa PAO1
ComponentsBeta-lactamase
KeywordsHYDROLASE / beta-lactamase fold / antibiotic resistance
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
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsBenvenuti, M. / De Luca, F. / Docquier, J.D. / Mangani, S.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2013
Title: Structural insight into potent broad-spectrum inhibition with reversible recyclization mechanism: avibactam in complex with CTX-M-15 and Pseudomonas aeruginosa AmpC beta-lactamases
Authors: Lahiri, S.D. / Mangani, S. / Durand-Reville, T. / Benvenuti, M. / De Luca, F. / Sanyal, G. / Docquier, J.D.
History
DepositionSep 6, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Database references
Revision 1.2Nov 8, 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

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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)40,7862
Polymers40,7241
Non-polymers621
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.060, 83.060, 122.420
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Beta-lactamase / Cephalosporinase


Mass: 40723.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: ampC, blaAmpC, PA4110 / Plasmid: pET-AmpC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P24735, beta-lactamase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.99 Å3/Da / Density % sol: 58.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M Tris, 20% PEG 8000, O.1M K2HPO4, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.936 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 5, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.936 Å / Relative weight: 1
ReflectionResolution: 1.79→46.617 Å / Num. all: 38317 / Num. obs: 38317 / % possible obs: 83.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 26.695 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 8.7
Reflection shellResolution: 1.79→1.89 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 1.8 / Num. unique all: 9784 / % possible all: 82.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KE4

1ke4


Resolution: 1.79→34.51 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / SU B: 6.065 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24384 1975 5.2 %RANDOM
Rwork0.19016 ---
obs0.19296 36340 82.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.534 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.132 Å
Refinement stepCycle: LAST / Resolution: 1.79→34.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2839 0 4 231 3074
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222913
X-RAY DIFFRACTIONr_angle_refined_deg2.0291.9743961
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6975366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.1123.433134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.57715455
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.21524
X-RAY DIFFRACTIONr_chiral_restr0.180.2423
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212279
X-RAY DIFFRACTIONr_mcbond_it1.2071.51827
X-RAY DIFFRACTIONr_mcangle_it1.95122912
X-RAY DIFFRACTIONr_scbond_it3.48331086
X-RAY DIFFRACTIONr_scangle_it5.3584.51049
LS refinement shellResolution: 1.79→1.836 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 137 -
Rwork0.291 2573 -
obs--78.89 %
Refinement TLS params.Method: refined / Origin x: -35.2493 Å / Origin y: 12.2298 Å / Origin z: -14.3113 Å
111213212223313233
T0.0528 Å20.0065 Å2-0.008 Å2-0.0122 Å2-0.0063 Å2--0.0524 Å2
L0.3753 °2-0.0652 °20.0916 °2-1.205 °20.5195 °2--1.0969 °2
S-0.0376 Å °-0.0398 Å °-0.0052 Å °0.0039 Å °0.0762 Å °-0.077 Å °-0.054 Å °0.0738 Å °-0.0386 Å °

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