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- PDB-7mee: CDD-1 beta-lactamase in imidazole/MPD 6 minute avibactam complex -

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Basic information

Entry
Database: PDB / ID: 7mee
TitleCDD-1 beta-lactamase in imidazole/MPD 6 minute avibactam complex
ComponentsBeta-lactamase
KeywordsHYDROLASE/INHIBITOR / Gram-positive / beta-lactamase / antibiotic resistance / inhibitor / avibactam / 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: 1.88 Å
AuthorsSmith, C.A. / Vakulenko, S.B.
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
DepositionApr 6, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _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)29,2927
Polymers28,5741
Non-polymers7186
Water2,522140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.323, 123.323, 123.323
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-403-

SO4

31A-599-

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: 28574.234 Da / Num. of mol.: 1 / Mutation: K238A, K244A
Source method: isolated from a genetically manipulated source
Details: double lysine to alanine mutant Lys238Ala and Lys244Ala
Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: blaR1_1, E5F32_07085, E5F39_11445, SAMEA3374989_01677 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A160YKM3, beta-lactamase

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Non-polymers , 5 types, 146 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.: 3 / 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.: 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: 2.73 Å3/Da / Density % sol: 55.03 %
Crystal growTemperature: 277 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: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.88→39 Å / Num. obs: 26789 / % possible obs: 99.7 % / Redundancy: 21.2 % / CC1/2: 0.999 / Rpim(I) all: 0.03 / Rrim(I) all: 0.139 / Net I/σ(I): 13.2
Reflection shellResolution: 1.88→1.92 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 1590 / CC1/2: 0.8 / Rpim(I) all: 0.377

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.88→39 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2159 1357 5.08 %
Rwork0.1875 25369 -
obs0.189 26726 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.03 Å2 / Biso mean: 34.4439 Å2 / Biso min: 18.99 Å2
Refinement stepCycle: final / Resolution: 1.88→39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2009 0 43 143 2195
Biso mean--49.87 39.01 -
Num. residues----250
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072129
X-RAY DIFFRACTIONf_angle_d1.0162878
X-RAY DIFFRACTIONf_dihedral_angle_d12.615296
X-RAY DIFFRACTIONf_chiral_restr0.061307
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 (%)
1.88-1.940.30361200.26682392251297
1.94-2.020.23911230.204725122635100
2.02-2.110.25941290.192224822611100
2.11-2.220.22681310.196125152646100
2.22-2.360.26461370.206325122649100
2.36-2.550.2531470.20524962643100
2.55-2.80.23971400.20125522692100
2.8-3.210.24921330.210625462679100
3.21-4.040.17811390.165826042743100
4.04-390.18991580.170427582916100

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