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- PDB-6s1s: Crystal structure of AmpC from Pseudomonas aeruginosa in complex ... -

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Basic information

Entry
Database: PDB / ID: 6s1s
TitleCrystal structure of AmpC from Pseudomonas aeruginosa in complex with [3-(2-carboxyvinyl)phenyl]boronic acid] inhibitor
ComponentsBeta-lactamase
KeywordsHYDROLASE / Inhibitor / Complex / AmpC
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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-KRT / PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsKekez, I. / Vicario, M. / Bellio, P. / Tosoni, E. / Celenza, G. / Blazquez, J. / Tondi, D. / Cendron, L.
CitationJournal: Antibiotics / Year: 2019
Title: Phenylboronic Acids Probing Molecular Recognition against Class A and Class C beta-lactamases.
Authors: Linciano, P. / Vicario, M. / Kekez, I. / Bellio, P. / Celenza, G. / Martin-Blecua, I. / Blazquez, J. / Cendron, L. / Tondi, D.
History
DepositionJun 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)43,7363
Polymers43,4491
Non-polymers2872
Water2,360131
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-2 kcal/mol
Surface area15160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.678, 82.678, 123.563
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


Mass: 43449.223 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: ampC, EFK27_12075, RW109_RW109_01564 / Production host: Escherichia coli (E. coli) / References: UniProt: Q541D8, beta-lactamase
#2: Chemical ChemComp-KRT / (~{E})-3-[3-(dihydroxyboranyl)phenyl]prop-2-enoic acid


Mass: 191.976 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H9BO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.81 Å3/Da / Density % sol: 56.16 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.7 / Details: 1.8 M potassium phosphate buffer, pH 8.7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97779 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97779 Å / Relative weight: 1
ReflectionResolution: 1.78→46.78 Å / Num. obs: 46605 / % possible obs: 97.8 % / Redundancy: 3.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Net I/σ(I): 12.6
Reflection shellResolution: 1.78→1.81 Å / Num. unique obs: 2490

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GZB

4gzb


Resolution: 1.78→46.78 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.966 / SU B: 3.02 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.095 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20028 2322 5 %RANDOM
Rwork0.1766 ---
obs0.1778 44242 97.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.297 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.78→46.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2843 0 19 131 2993
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0142962
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172635
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.6654038
X-RAY DIFFRACTIONr_angle_other_deg0.9891.6326188
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7575376
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.2321.553161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.95715465
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5271524
X-RAY DIFFRACTIONr_chiral_restr0.0860.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023407
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02543
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1513.6421477
X-RAY DIFFRACTIONr_mcbond_other3.1313.641476
X-RAY DIFFRACTIONr_mcangle_it4.1175.4431847
X-RAY DIFFRACTIONr_mcangle_other4.1225.4471848
X-RAY DIFFRACTIONr_scbond_it4.6174.2281485
X-RAY DIFFRACTIONr_scbond_other4.6084.2181482
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.8216.1012179
X-RAY DIFFRACTIONr_long_range_B_refined7.76842.5623251
X-RAY DIFFRACTIONr_long_range_B_other7.77942.4483232
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.777→1.823 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 150 -
Rwork0.337 3115 -
obs--93.71 %

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