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- PDB-7lnq: Structure of the avibactam-CDD-1 3 minute complex in imidazole and MPD -

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Basic information

Entry
Database: PDB / ID: 7lnq
TitleStructure of the avibactam-CDD-1 3 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
CARBON DIOXIDE / Chem-NXL / Beta-lactamase
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.73 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 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)36,8578
Polymers36,0431
Non-polymers8147
Water3,243180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-46 kcal/mol
Surface area11490 Å2
Unit cell
Length a, b, c (Å)123.548, 123.548, 123.548
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-403-

SO4

21A-619-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 36043.055 Da / Num. of mol.: 1 / Mutation: K238A, K244A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (bacteria)
Gene: blaR1_4, blaR1_1, E5F39_11445, SAMEA2239407_03320, SAMEA3374989_01677
Production host: Escherichia coli (E. coli) / References: UniProt: A0A160YKM3, beta-lactamase

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Non-polymers , 5 types, 187 molecules

#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-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.18 Å3/Da / Density % sol: 43.58 %
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: Jun 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.73→39.1 Å / Num. obs: 34244 / % possible obs: 100 % / Redundancy: 23.6 % / CC1/2: 0.999 / Rpim(I) all: 0.023 / Rrim(I) all: 0.111 / Net I/σ(I): 18.9
Reflection shellResolution: 1.73→1.76 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 1839 / CC1/2: 0.753 / Rpim(I) all: 0.44

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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: 1.73→39.07 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2132 1648 4.82 %
Rwork0.1847 32541 -
obs0.1861 34189 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.65 Å2 / Biso mean: 30.923 Å2 / Biso min: 16.12 Å2
Refinement stepCycle: final / Resolution: 1.73→39.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2017 0 48 184 2249
Biso mean--42.65 38.51 -
Num. residues----251
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082162
X-RAY DIFFRACTIONf_angle_d1.032928
X-RAY DIFFRACTIONf_dihedral_angle_d11.771314
X-RAY DIFFRACTIONf_chiral_restr0.061312
X-RAY DIFFRACTIONf_plane_restr0.007371
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.73-1.780.30721220.250726712793
1.78-1.840.27561280.22226622790
1.84-1.90.27841340.245926612795
1.9-1.980.2461150.203726692784
1.98-2.070.21961320.17926922824
2.07-2.180.20071430.180826552798
2.18-2.320.20371380.192626902828
2.32-2.50.231410.194526872828
2.5-2.750.22271360.187827252861
2.75-3.140.22481530.19527162869
3.14-3.960.19421460.164127692915
3.96-39.070.19621600.173929443104

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