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- PDB-7lnr: Structure of the avibactam-CDD-1 120 minute complex in imidazole ... -

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Basic information

Entry
Database: PDB / ID: 7lnr
TitleStructure of the avibactam-CDD-1 120 minute complex in imidazole and MPD
ComponentsBeta-lactamase
KeywordsHYDROLASE/INHIBITOR / beta-lactamase / antibiotic resistance / HYDROLASE / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / membrane
Similarity search - Function
Beta-lactamase, class-D active site / Beta-lactamase class-D active site. / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Chem-NXL / Beta-lactamase
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.83 Å
AuthorsSmith, C.A. / Vakulenko, S.B. / Stewart, N.K.
CitationJournal: Acs Infect Dis. / Year: 2021
Title: In Crystallo Time-Resolved Interaction of the Clostridioides difficile CDD-1 enzyme with Avibactam Provides New Insights into the Catalytic Mechanism of Class D beta-lactamases.
Authors: Stewart, N.K. / Toth, M. / Stasyuk, A. / Vakulenko, S.B. / Smith, C.A.
History
DepositionFeb 8, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: 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 1.2Oct 18, 2023Group: 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 1.3Oct 23, 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)36,6746
Polymers36,0001
Non-polymers6745
Water2,720151
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint-31 kcal/mol
Surface area11520 Å2
Unit cell
Length a, b, c (Å)124.083, 124.083, 124.083
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number212
Space group name H-MP4332
Components on special symmetry positions
IDModelComponents
11A-625-

HOH

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Components

#1: Protein Beta-lactamase / CDD-1 beta-lactamase


Mass: 36000.055 Da / Num. of mol.: 1 / Mutation: K238A, K244A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (bacteria)
Gene: blaR1_1, blaR1_4, E5F39_11445, SAMEA2239407_03320, SAMEA3374989_01677
Production host: Escherichia coli (E. coli) / References: UniProt: A0A160YKM3, 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 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.21 Å3/Da / Density % sol: 44.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M HEPES, 2.4 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.83→39.24 Å / Num. obs: 29368 / % possible obs: 99.9 % / Redundancy: 25.7 % / CC1/2: 0.999 / Rpim(I) all: 0.02 / Rrim(I) all: 0.099 / Net I/σ(I): 21.5
Reflection shellResolution: 1.83→1.87 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 1759 / CC1/2: 0.69 / Rpim(I) all: 0.402

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
REFMACrefinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6EDM

6edm


Resolution: 1.83→39.24 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2338 1421 4.85 %
Rwork0.1973 27871 -
obs0.199 29292 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.68 Å2 / Biso mean: 33.7021 Å2 / Biso min: 18.26 Å2
Refinement stepCycle: final / Resolution: 1.83→39.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2009 0 55 153 2217
Biso mean--46.62 38.74 -
Num. residues----250
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082129
X-RAY DIFFRACTIONf_angle_d1.032880
X-RAY DIFFRACTIONf_dihedral_angle_d13.667303
X-RAY DIFFRACTIONf_chiral_restr0.065307
X-RAY DIFFRACTIONf_plane_restr0.006365
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.83-1.90.41071460.36442691283799
1.9-1.970.31441370.260627462883100
1.97-2.060.26061450.203627192864100
2.06-2.170.24531400.203327592899100
2.17-2.310.24751480.208127242872100
2.31-2.490.26171480.215127562904100
2.49-2.740.24361410.205127722913100
2.74-3.130.25581220.212828322954100
3.13-3.940.21441370.179728442981100
3.95-39.240.19861570.173930283185100

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