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- PDB-6g9s: Structural basis for the inhibition of E. coli PBP2 -

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Basic information

Entry
Database: PDB / ID: 6g9s
TitleStructural basis for the inhibition of E. coli PBP2
ComponentsPeptidoglycan D,D-transpeptidase MrdA
KeywordsHYDROLASE/ANTIBIOTIC / penicillin binding protein / HYDROLASE-ANTIBIOTIC complex
Function / homology
Function and homology information


peptidoglycan L,D-transpeptidase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / outer membrane-bounded periplasmic space / response to antibiotic / proteolysis / plasma membrane
Similarity search - Function
Penicillin-binding protein 2 / Penicillin-binding protein, dimerisation domain / Penicillin-binding Protein dimerisation domain / Penicillin-binding protein, dimerisation domain superfamily / : / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like ...Penicillin-binding protein 2 / Penicillin-binding protein, dimerisation domain / Penicillin-binding Protein dimerisation domain / Penicillin-binding protein, dimerisation domain superfamily / : / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-ET5 / Peptidoglycan D,D-transpeptidase MrdA
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 Å
AuthorsRuff, M. / Levy, N.
CitationJournal: J.Med.Chem. / Year: 2019
Title: Structural Basis for E. coli Penicillin Binding Protein (PBP) 2 Inhibition, a Platform for Drug Design.
Authors: Levy, N. / Bruneau, J.M. / Le Rouzic, E. / Bonnard, D. / Le Strat, F. / Caravano, A. / Chevreuil, F. / Barbion, J. / Chasset, S. / Ledoussal, B. / Moreau, F. / Ruff, M.
History
DepositionApr 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.2Jan 17, 2024Group: 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 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidoglycan D,D-transpeptidase MrdA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4102
Polymers65,0761
Non-polymers3341
Water6,557364
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area24200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.303, 182.806, 75.561
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-963-

HOH

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Components

#1: Protein Peptidoglycan D,D-transpeptidase MrdA / Penicillin-binding protein 2 / PBP-2


Mass: 65075.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Serine 330 covalently modified with ligand / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: mrdA, pbpA, b0635, JW0630 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: P0AD65, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical ChemComp-ET5 / (3~{R},6~{S})-6-(aminomethyl)-4-(1,3-oxazol-5-yl)-3-(sulfooxyamino)-3,6-dihydro-2~{H}-pyridine-1-carboxylic acid


Mass: 334.306 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N4O7S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / Source method: isolated from a natural source / Formula: H2O
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: 3.6 Å3/Da / Density % sol: 65.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M TrisBase / Bicine pH 8,5 ; 0.1 M Carboxylic acids mix (0.02 M Sodium formate ; 0.02 M Ammonium acetate ; 0.02 M Sodium citrate tribasic dihydrate ; 0.02 M Sodium potassium tartrate ...Details: 0.1 M TrisBase / Bicine pH 8,5 ; 0.1 M Carboxylic acids mix (0.02 M Sodium formate ; 0.02 M Ammonium acetate ; 0.02 M Sodium citrate tribasic dihydrate ; 0.02 M Sodium potassium tartrate tetrahydrate ; 0.02 M Sodium oxamate) ; 24 % Glycerol ; 12 % PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→45.7 Å / Num. obs: 59191 / % possible obs: 92.84 % / Redundancy: 11.3 % / CC1/2: 0.995 / Rpim(I) all: 0.05733 / Rrim(I) all: 0.1985 / Net I/σ(I): 8.32
Reflection shellResolution: 2→2.07 Å / Redundancy: 10.4 % / Rmerge(I) obs: 3.254 / Num. unique obs: 4729 / CC1/2: 0.57 / Rpim(I) all: 1.054 / Rrim(I) all: 3.424 / % possible all: 80.6

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ensemble of models was used: 5e31, 5dvy, 1vqq, 3ocl, 4ool, 4wek, 4wej, 4mnr, 1xkw

5e31

5dvy

1vqq

3ocl

4ool

4wek

4wej

4mnr

1xkw


Resolution: 2.001→44.405 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 33.03
RfactorNum. reflection% reflection
Rfree0.2596 1860 3.38 %
Rwork0.2159 --
obs0.2173 55067 92.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.001→44.405 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4275 0 0 364 4639
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084383
X-RAY DIFFRACTIONf_angle_d0.9445961
X-RAY DIFFRACTIONf_dihedral_angle_d4.1342618
X-RAY DIFFRACTIONf_chiral_restr0.052644
X-RAY DIFFRACTIONf_plane_restr0.006774
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0009-2.0550.47931180.46283479X-RAY DIFFRACTION79
2.055-2.11550.44211210.41653662X-RAY DIFFRACTION84
2.1155-2.18380.41671290.38433752X-RAY DIFFRACTION86
2.1838-2.26180.37281360.33934011X-RAY DIFFRACTION91
2.2618-2.35240.38731390.31693990X-RAY DIFFRACTION91
2.3524-2.45940.32541450.28573984X-RAY DIFFRACTION91
2.4594-2.58910.30341480.25864100X-RAY DIFFRACTION94
2.5891-2.75130.32291500.23814178X-RAY DIFFRACTION95
2.7513-2.96370.27941480.21344264X-RAY DIFFRACTION97
2.9637-3.26180.25641520.20844321X-RAY DIFFRACTION98
3.2618-3.73360.22261560.18264401X-RAY DIFFRACTION99
3.7336-4.70310.21461550.14094438X-RAY DIFFRACTION99
4.7031-44.41590.16161630.15224627X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 29.2097 Å / Origin y: 55.0645 Å / Origin z: 38.9349 Å
111213212223313233
T0.1922 Å2-0.0501 Å2-0.0185 Å2-0.19 Å20.0112 Å2--0.1258 Å2
L1.0753 °20.8641 °20.1593 °2-1.1735 °20.0056 °2---0.0022 °2
S-0.0057 Å °0.0202 Å °0.0222 Å °-0.0116 Å °0.0105 Å °-0.0029 Å °0.0404 Å °-0.0255 Å °0.0002 Å °
Refinement TLS groupSelection details: all

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