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- PDB-6fm7: Crystal structure of the class C beta-lactamase TRU-1 from Aeromo... -

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Basic information

Entry
Database: PDB / ID: 6fm7
TitleCrystal structure of the class C beta-lactamase TRU-1 from Aeromonas enteropelogenes in complex with avibactam
ComponentsBeta-lactamase
KeywordsHYDROLASE / avibactam / NXL / serine beta-lactamase / TRU-1 / class C / 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
Chem-NXL / Beta-lactamase / Beta-lactamase
Similarity search - Component
Biological speciesAeromonas enteropelogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.04 Å
AuthorsPozzi, C. / De Luca, F. / Benvenuti, M. / Di Pisa, F. / 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 ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)42,4056
Polymers41,8221
Non-polymers5845
Water9,296516
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area600 Å2
ΔGint-27 kcal/mol
Surface area14420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.552, 78.248, 48.306
Angle α, β, γ (deg.)90.00, 106.54, 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-NXL / (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide / avibactam, bound form / NXL104, bound form


Mass: 267.260 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H13N3O6S / Comment: antibiotic*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 516 / 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: 2.11 Å3/Da / Density % sol: 41.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 25% 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: ID23-1 / Wavelength: 0.9834 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 25, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9834 Å / Relative weight: 1
ReflectionResolution: 1.04→46.33 Å / Num. obs: 153026 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Biso Wilson estimate: 6.525 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rrim(I) all: 0.062 / Net I/σ(I): 17.6
Reflection shellResolution: 1.04→1.1 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 4.7 / Num. unique obs: 20705 / CC1/2: 0.934 / Rrim(I) all: 0.379 / % possible all: 91.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FM6

6fm6


Resolution: 1.04→46.31 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.976 / Rfactor Rfree error: 0.022 / SU B: 0.498 / SU ML: 0.013 / SU R Cruickshank DPI: 0.0213 / Cross valid method: THROUGHOUT / ESU R: 0.021 / ESU R Free: 0.022 / SU Rfree Cruickshank DPI: 0.0224 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13623 7664 5 %RANDOM
Rwork0.11637 ---
obs0.11735 145332 98.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 10.812 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20.01 Å2
2--0 Å20 Å2
3----0.02 Å2
Refine analyzeLuzzati coordinate error obs: 0.109 Å
Refinement stepCycle: 1 / Resolution: 1.04→46.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2726 0 35 516 3277
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193035
X-RAY DIFFRACTIONr_bond_other_d0.0020.022788
X-RAY DIFFRACTIONr_angle_refined_deg1.4241.9724172
X-RAY DIFFRACTIONr_angle_other_deg0.92936494
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3695422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.81123.788132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.29115495
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0621519
X-RAY DIFFRACTIONr_chiral_restr0.0850.2458
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213473
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02631
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_it0.8261500
X-RAY DIFFRACTIONr_mcbond_other0.8261499
X-RAY DIFFRACTIONr_mcangle_it1.0371893
X-RAY DIFFRACTIONr_mcangle_other1.0371894
X-RAY DIFFRACTIONr_scbond_it0.8021535
X-RAY DIFFRACTIONr_scbond_other0.7991535
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.0812249
X-RAY DIFFRACTIONr_long_range_B_refined2.3093654
X-RAY DIFFRACTIONr_long_range_B_other1.6933498
X-RAY DIFFRACTIONr_rigid_bond_restr0.92632452
X-RAY DIFFRACTIONr_sphericity_free20.3115288
X-RAY DIFFRACTIONr_sphericity_bonded7.58152600
LS refinement shellResolution: 1.04→1.067 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.195 446 -
Rwork0.19 9346 -
obs--85.77 %

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