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- PDB-4hef: Structure of avibactam bound to Pseudomonas aeruginosa AmpC -

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Basic information

Entry
Database: PDB / ID: 4hef
TitleStructure of avibactam bound to Pseudomonas aeruginosa AmpC
ComponentsBeta-lactamase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / b-lactamase / hydrolase / periplasmic protein / HYDROLASE-HYDROLASE INHIBITOR complex
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-NXL / Beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsLahiri, S.D.
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
DepositionOct 3, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2015Group: Non-polymer description
Revision 1.2Feb 7, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.3Sep 16, 2020Group: Database references / Derived calculations / Structure summary
Category: chem_comp / struct ...chem_comp / struct / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _struct.title ..._chem_comp.pdbx_synonyms / _struct.title / _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_ref_seq_dif.details / _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)39,9934
Polymers39,5421
Non-polymers4513
Water6,143341
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.880, 71.200, 106.250
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-lactamase / / Cephalosporinase


Mass: 39541.641 Da / Num. of mol.: 1 / Fragment: UNP residues 29-388
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: ampC, PA4110 / Production host: Escherichia coli (E. coli) / References: UniProt: P24735, beta-lactamase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-NXL / (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide / avibactam, bound form / NXL104, bound form / Avibactam


Mass: 267.260 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H13N3O6S / Comment: antibiotic, inhibitor*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 341 / 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: 2.15 Å3/Da / Density % sol: 42.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris (pH 8.0), 20% PEG 8000, 0.1M K2HSO4 , VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ DW
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Jan 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.86→44.88 Å / Num. all: 28887 / Num. obs: 28777 / % possible obs: 98.1 % / Redundancy: 5.1 % / Biso Wilson estimate: 17.77 Å2

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
d*TREKdata reduction
SCALAdata scaling
AMoREphasing
BUSTER2.11.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→23.11 Å / Cor.coef. Fo:Fc: 0.9316 / Cor.coef. Fo:Fc free: 0.9134 / Occupancy max: 1 / Occupancy min: 0.2 / SU R Cruickshank DPI: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2015 1461 5.08 %RANDOM
Rwork0.1744 ---
obs0.1758 28777 98.11 %-
all-28887 --
Displacement parametersBiso max: 116.89 Å2 / Biso mean: 18.6529 Å2 / Biso min: 3.42 Å2
Baniso -1Baniso -2Baniso -3
1-5.1377 Å20 Å20 Å2
2---0.2122 Å20 Å2
3----4.9255 Å2
Refine analyzeLuzzati coordinate error obs: 0.195 Å
Refinement stepCycle: LAST / Resolution: 1.86→23.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2793 0 29 341 3163
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012930HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.013992HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1009SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes68HARMONIC2
X-RAY DIFFRACTIONt_gen_planes439HARMONIC5
X-RAY DIFFRACTIONt_it2930HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.99
X-RAY DIFFRACTIONt_other_torsion14.89
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion362SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3813SEMIHARMONIC4
LS refinement shellResolution: 1.86→1.93 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.266 134 4.93 %
Rwork0.2294 2584 -
all0.2311 2718 -
obs--98.11 %
Refinement TLS params.Method: refined / Origin x: -6.206 Å / Origin y: -2.987 Å / Origin z: 17.7378 Å
111213212223313233
T0.0065 Å2-0.0035 Å20.0093 Å2--0.0664 Å2-0.0079 Å2---0.0599 Å2
L0.4091 °2-0.0536 °20.0328 °2-0.4118 °2-0.0885 °2--0.634 °2
S-0.0044 Å °-0.0552 Å °-0.0105 Å °0.0255 Å °0.0127 Å °0.0067 Å °-0.0145 Å °-0.0135 Å °-0.0082 Å °
Refinement TLS groupSelection details: { A|* }

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