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- PDB-7me9: CDD-1 beta-lactamase in imidazole/MPD 30 seconds avibactam complex -

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Basic information

Entry
Database: PDB / ID: 7me9
TitleCDD-1 beta-lactamase in imidazole/MPD 30 seconds avibactam complex
ComponentsBeta-lactamase
KeywordsHYDROLASE / Gram-positive / beta-lactamase / antibiotic resistance / inhibitor / avibactam
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
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 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 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 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)29,2167
Polymers28,6171
Non-polymers5986
Water3,171176
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.489, 123.489, 123.489
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-402-

SO4

21A-402-

SO4

31A-623-

HOH

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Components

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


Mass: 28617.234 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
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.74 Å3/Da / Density % sol: 55.14 %
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: Jun 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.7→39.1 Å / Num. obs: 36007 / % possible obs: 100 % / Redundancy: 23.6 % / CC1/2: 0.999 / Rpim(I) all: 0.023 / Rrim(I) all: 0.11 / Net I/σ(I): 20.7
Reflection shellResolution: 1.7→1.73 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1853 / CC1/2: 0.776 / Rpim(I) all: 0.35

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Processing

Software
NameVersionClassification
PHENIXdev_3908refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 7LNO

7lno


Resolution: 1.7→37.23 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 20.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.205 1749 4.87 %
Rwork0.1783 34197 -
obs0.1797 35946 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.6 Å2 / Biso mean: 27.8896 Å2 / Biso min: 14.47 Å2
Refinement stepCycle: final / Resolution: 1.7→37.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2012 0 33 177 2222
Biso mean--50.09 34.09 -
Num. residues----250
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072125
X-RAY DIFFRACTIONf_angle_d0.9842876
X-RAY DIFFRACTIONf_dihedral_angle_d10.972293
X-RAY DIFFRACTIONf_chiral_restr0.062305
X-RAY DIFFRACTIONf_plane_restr0.006365
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
1.7-1.750.29721510.229527802931
1.75-1.810.24031350.214127992934
1.81-1.870.24551400.197127972937
1.87-1.950.2381270.190928042931
1.95-2.030.23041270.175128382965
2.03-2.140.20531480.179328042952
2.14-2.280.1931520.18228242976
2.28-2.450.20261400.189128262966
2.45-2.70.21191550.188328453000
2.7-3.090.23841550.192728753030
3.09-3.890.19241500.16529203070
3.89-37.230.17461690.161230853254

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