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- PDB-6pq8: Crystal structure of TLA-1 S70G extended spectrum Beta-lactamase ... -

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Basic information

Entry
Database: PDB / ID: 6pq8
TitleCrystal structure of TLA-1 S70G extended spectrum Beta-lactamase in complex with clavulanic acid
ComponentsBeta-lactamase
Keywordshydrolase/hydrolase inhibitor / Lactamase / Antibiotic / Resistance / Hydrolase / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / ASPARTIC ACID / Chem-J01 / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsRudino-Pinera, E. / Cifuentes-Castro, V.H. / Rodriguez-Almazan, C.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: The crystal structure of ESBL TLA-1 in complex with clavulanic acid reveals a second acylation site.
Authors: Cifuentes-Castro, V. / Rodriguez-Almazan, C. / Silva-Sanchez, J. / Rudino-Pinera, E.
History
DepositionJul 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Oct 11, 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

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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)34,75118
Polymers33,3421
Non-polymers1,40917
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.410, 99.410, 99.470
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Beta-lactamase


Mass: 33342.285 Da / Num. of mol.: 1 / Mutation: S70G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: tla-1 / Plasmid: pJ411 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9X6W1, beta-lactamase

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Non-polymers , 7 types, 200 molecules

#2: Chemical ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7NO4
#3: Chemical ChemComp-J01 / (2R,3Z,5R)-3-(2-HYDROXYETHYLIDENE)-7-OXO-4-OXA-1-AZABICYCLO[3.2.0]HEPTANE-2-CARBOXYLIC ACID / CLAVULANIC ACID


Mass: 199.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H9NO5 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic, inhibitor*YM
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.97 Å3/Da / Density % sol: 69.05 %
Crystal growTemperature: 291.5 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 2.4 M Ammonium Sulfate, 100 mM Sodium Phosphate dibasic / Citric acid pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9793326 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 17, 2018 / Details: Sagitally focusing 2nd crystal
RadiationMonochromator: Si (111) Rosenbaum-Rock double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793326 Å / Relative weight: 1
ReflectionResolution: 2.2→19.89 Å / Num. obs: 27771 / % possible obs: 100 % / Redundancy: 11.27 % / Biso Wilson estimate: 39.27 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.08 / Rrim(I) all: 0.082 / Rsym value: 0.082 / Net I/σ(I): 32.6
Reflection shellResolution: 2.2→2.3 Å / Rmerge(I) obs: 1.46 / Num. unique obs: 1820 / CC1/2: 0.814 / Rrim(I) all: 1.49 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.12_2829refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NVU

6nvu


Resolution: 2.2→19.89 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.77
RfactorNum. reflection% reflection
Rfree0.2258 1227 4.75 %
Rwork0.1838 --
obs0.1859 25854 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 100.26 Å2 / Biso mean: 41.4853 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.2→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2176 0 87 183 2446
Biso mean--60.98 46.51 -
Num. residues----276
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072310
X-RAY DIFFRACTIONf_angle_d0.9153119
X-RAY DIFFRACTIONf_chiral_restr0.06353
X-RAY DIFFRACTIONf_plane_restr0.005391
X-RAY DIFFRACTIONf_dihedral_angle_d5.481916
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.2-2.2880.3541290.31672668
2.288-2.39190.35311150.27232724
2.3919-2.51780.29871280.25332686
2.5178-2.67520.27151500.23222687
2.6752-2.88120.26711490.20732683
2.8812-3.17010.24861370.20092745
3.1701-3.62640.21491270.17052740
3.6264-4.55980.19181410.13382779
4.5598-19.890.17151510.15822915

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