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- PDB-6fm6: Crystal structure of the class C beta-lactamase TRU-1 from Aeromo... -

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Basic information

Entry
Database: PDB / ID: 6fm6
TitleCrystal structure of the class C beta-lactamase TRU-1 from Aeromonas enteropelogenes
ComponentsBeta-lactamase
KeywordsHYDROLASE / class C / serine beta-lactamase / TRU-1 / Aeromonas enteropelogenes
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
TRIETHYLENE GLYCOL / Beta-lactamase / Beta-lactamase
Similarity search - Component
Biological speciesAeromonas enteropelogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsPozzi, C. / De Luca, F. / Di Pisa, F. / Benvenuti, M. / Docquier, J.D. / Mangani, S.
CitationJournal: ChemMedChem / Year: 2018
Title: Atomic-Resolution Structure of a Class C beta-Lactamase and Its Complex with Avibactam.
Authors: Pozzi, C. / Di Pisa, F. / De Luca, F. / Benvenuti, M. / Docquier, J.D. / Mangani, S.
History
DepositionJan 30, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.name
Revision 1.2Aug 29, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 17, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2605
Polymers41,8221
Non-polymers4384
Water11,836657
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-41 kcal/mol
Surface area14690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.885, 78.345, 48.190
Angle α, β, γ (deg.)90.00, 106.63, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase /


Mass: 41821.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeromonas enteropelogenes (bacteria) / Gene: ampC / Plasmid: pET-TRU-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: B2BSN6, UniProt: A0A175VLQ4*PLUS, beta-lactamase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 657 / 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: 1.98 Å3/Da / Density % sol: 38.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 30% wt/vol PEG-8000, 0.2 M ammonium sulfate and 0.1 M sodium cacodylate, pH 6.5
PH range: 6.5-7.5 / Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 20, 2007
RadiationMonochromator: Diamond (001) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.05→38.35 Å / Num. obs: 141631 / % possible obs: 93.5 % / Redundancy: 3.6 % / Biso Wilson estimate: 5.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Rrim(I) all: 0.043 / Net I/σ(I): 18.2
Reflection shellResolution: 1.05→1.11 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.114 / Mean I/σ(I) obs: 4.7 / Num. unique obs: 15018 / CC1/2: 0.967 / Rrim(I) all: 0.155 / % possible all: 68

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GZB

4gzb


Resolution: 1.05→26.43 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.975 / Rfactor Rfree error: 0.024 / SU B: 0.56 / SU ML: 0.014 / SU R Cruickshank DPI: 0.0236 / Cross valid method: THROUGHOUT / ESU R: 0.024 / ESU R Free: 0.024 / SU Rfree Cruickshank DPI: 0.0235 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.12944 7107 5 %RANDOM
Rwork0.11438 ---
obs0.11513 134487 93.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 8.587 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.105 Å
Refinement stepCycle: 1 / Resolution: 1.05→26.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2742 0 22 657 3421
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193167
X-RAY DIFFRACTIONr_bond_other_d0.0020.022923
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.9674357
X-RAY DIFFRACTIONr_angle_other_deg0.98236818
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7135439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.4423.448145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.21315529
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8781524
X-RAY DIFFRACTIONr_chiral_restr0.0890.2468
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213661
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02679
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_it0.631551
X-RAY DIFFRACTIONr_mcbond_other0.6311550
X-RAY DIFFRACTIONr_mcangle_it0.9541969
X-RAY DIFFRACTIONr_mcangle_other0.9541970
X-RAY DIFFRACTIONr_scbond_it0.7121616
X-RAY DIFFRACTIONr_scbond_other0.7061616
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.8892358
X-RAY DIFFRACTIONr_long_range_B_refined2.473856
X-RAY DIFFRACTIONr_long_range_B_other2.473857
X-RAY DIFFRACTIONr_rigid_bond_restr1.57532391
X-RAY DIFFRACTIONr_sphericity_free19.4275349
X-RAY DIFFRACTIONr_sphericity_bonded8.58652629
LS refinement shellResolution: 1.05→1.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.187 327 -
Rwork0.176 6317 -
obs--59.52 %

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