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- PDB-7ker: avibactam-CDD-1 45 minute complex -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 7ker
Titleavibactam-CDD-1 45 minute complex
ComponentsBeta-lactamase
KeywordsHYDROLASE/INHIBITOR / antibiotic resistance / mutant / Gram-positive / inhibitor / 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-FYG / Chem-NXL / Beta-lactamase
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.93 Å
AuthorsSmith, C.A. / Vakulenko, S.B. / Stewart, N.K. / Toth, M.
CitationJournal: Acs Infect Dis. / Year: 2021
Title: Inhibition of the Clostridioides difficile Class D beta-Lactamase CDD-1 by Avibactam.
Authors: Stewart, N.K. / Toth, M. / Stasyuk, A. / Lee, M. / Smith, C.A. / Vakulenko, S.B.
History
DepositionOct 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1May 26, 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 1.2Apr 2, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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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)37,41210
Polymers36,0431
Non-polymers1,3699
Water2,522140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-52 kcal/mol
Surface area11390 Å2
Unit cell
Length a, b, c (Å)124.184, 124.184, 124.184
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-405-

SO4

21A-405-

SO4

31A-591-

HOH

41A-634-

HOH

51A-640-

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
Details: Class D beta-lactamase / 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 , 6 types, 149 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-FYG / (2S,5R)-7-oxo-6-(sulfooxy)-1,6-diazabicyclo[3.2.1]octane-2-carboxamide / Avibactam


Mass: 265.244 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H11N3O6S
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 44.44 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES, pH 7.0, 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: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.93→39.3 Å / Num. obs: 25361 / % possible obs: 99.8 % / Redundancy: 21 % / CC1/2: 0.998 / Rpim(I) all: 0.04 / Rrim(I) all: 0.186 / Net I/σ(I): 9.9
Reflection shellResolution: 1.93→1.97 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1645 / CC1/2: 0.751 / Rpim(I) all: 0.386

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Processing

Software
NameVersionClassification
PHENIXdev_3908refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.93→37.44 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1965 1286 5.1 %
Rwork0.1706 23914 -
obs0.172 25200 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.43 Å2 / Biso mean: 35.7738 Å2 / Biso min: 19.12 Å2
Refinement stepCycle: final / Resolution: 1.93→37.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2003 0 93 140 2236
Biso mean--52.7 42.04 -
Num. residues----251
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092186
X-RAY DIFFRACTIONf_angle_d1.2652974
X-RAY DIFFRACTIONf_dihedral_angle_d14.193338
X-RAY DIFFRACTIONf_chiral_restr0.066318
X-RAY DIFFRACTIONf_plane_restr0.007376
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.93-2.010.27211280.213925952723
2.01-2.10.22871440.18625972741
2.1-2.210.23551290.182526192748
2.21-2.350.23371400.180926112751
2.35-2.530.24851490.189226182767
2.53-2.780.2371540.189526292783
2.78-3.180.2381370.188526732810
3.19-4.010.15261420.147727082850
4.01-37.440.16531630.158828643027

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