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- PDB-7lno: Structure of apo-CDD-1 beta-lactamase in imidazole and MPD -

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Basic information

Entry
Database: PDB / ID: 7lno
TitleStructure of apo-CDD-1 beta-lactamase in imidazole and MPD
ComponentsBeta-lactamase
KeywordsHYDROLASE / beta-lactamase / antibiotic resistance
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: 1.58 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)36,8349
Polymers36,0431
Non-polymers7918
Water4,125229
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.321, 123.321, 123.321
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-655-

HOH

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Components

#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
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / 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.: 229 / 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: 2.17 Å3/Da / Density % sol: 43.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M HEPES, 2.4 M ammonium sulfate. Crystals transferred to 0.1 M imidazole pH 7.0, 85% 2-methyl-2,4-pentandiol (MPD)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.58→39 Å / Num. obs: 44557 / % possible obs: 99.6 % / Redundancy: 42.6 % / CC1/2: 1 / Rpim(I) all: 0.015 / Rrim(I) all: 0.098 / Net I/σ(I): 21.2
Reflection shellResolution: 1.58→1.6 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2038 / CC1/2: 0.841 / Rpim(I) all: 0.304

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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: 1.58→39 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.19 2174 4.91 %
Rwork0.1587 42127 -
obs0.1603 44301 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.26 Å2 / Biso mean: 30.0979 Å2 / Biso min: 17.32 Å2
Refinement stepCycle: final / Resolution: 1.58→39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2012 0 43 230 2285
Biso mean--61.35 40.57 -
Num. residues----250
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072144
X-RAY DIFFRACTIONf_angle_d0.9892908
X-RAY DIFFRACTIONf_dihedral_angle_d10.795296
X-RAY DIFFRACTIONf_chiral_restr0.063307
X-RAY DIFFRACTIONf_plane_restr0.007370
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.58-1.610.26241440.19332556270099
1.61-1.650.19291330.16225842717100
1.65-1.690.2291250.15226012726100
1.69-1.740.21461280.149825962724100
1.74-1.790.19931300.152425902720100
1.79-1.850.21381260.166126032729100
1.85-1.910.28691330.19552584271799
1.91-1.990.23721330.156226122745100
1.99-2.080.19461440.146325872731100
2.08-2.190.18891350.155526332768100
2.19-2.330.20181390.157626122751100
2.33-2.510.17851250.166926402765100
2.51-2.760.19081390.16826532792100
2.76-3.160.18391320.1826892821100
3.16-3.980.16131460.146127162862100
3.98-390.1891620.150128713033100

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