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

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Basic information

Entry
Database: PDB / ID: 7mea
TitleCDD-1 beta-lactamase in imidazole/MPD 1 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
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.
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

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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)29,4838
Polymers28,6171
Non-polymers8667
Water3,009167
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.668, 123.668, 123.668
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-618-

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-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.: 5 / 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.: 167 / Source method: isolated from a natural source / Formula: H2O
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: 2.75 Å3/Da / Density % sol: 55.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging 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: 1.73→39.1 Å / Num. obs: 34309 / % possible obs: 100 % / Redundancy: 21.4 % / CC1/2: 0.999 / Rpim(I) all: 0.022 / Rrim(I) all: 0.102 / Net I/σ(I): 19.2
Reflection shellResolution: 1.73→1.76 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 1852 / CC1/2: 0.753 / Rpim(I) all: 0.431

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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: 1.73→37.29 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2059 1657 4.83 %
Rwork0.1826 32645 -
obs0.1838 34302 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.01 Å2 / Biso mean: 31.5552 Å2 / Biso min: 17.58 Å2
Refinement stepCycle: final / Resolution: 1.73→37.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2012 0 49 168 2229
Biso mean--49.73 37.49 -
Num. residues----250
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082143
X-RAY DIFFRACTIONf_angle_d1.0222903
X-RAY DIFFRACTIONf_dihedral_angle_d12.247305
X-RAY DIFFRACTIONf_chiral_restr0.064309
X-RAY DIFFRACTIONf_plane_restr0.007367
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
1.73-1.780.27411270.226626692796
1.78-1.840.26181300.213726652795
1.84-1.90.26191300.205726872817
1.9-1.980.23221190.205426752794
1.98-2.070.23411290.181326852814
2.07-2.180.20081450.185626842829
2.18-2.320.19671390.185726852824
2.32-2.490.20671400.199327122852
2.5-2.750.22831380.19527202858
2.75-3.140.23331540.227272881
3.14-3.960.19091460.165227852931
3.96-37.290.17881600.167129513111

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