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- PDB-6g9p: Structural basis for the inhibition of E. coli PBP2 -

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Basic information

Entry
Database: PDB / ID: 6g9p
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 / outer membrane-bounded periplasmic space / regulation of cell shape / 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/transpeptidase-like
Similarity search - Domain/homology
Peptidoglycan D,D-transpeptidase MrdA
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.101 Å
AuthorsRuff, M. / Levy, N.
Citation
Journal: 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.
#1: Journal: Nat.Struct.Mol.Biol. / Year: 2019
Title: KMT9 monomethylates histone H4 lysine 12 and controls proliferation of prostate cancer cells.
Authors: Metzger, E. / Wang, S. / Urban, S. / Willmann, D. / Schmidt, A. / Offermann, A. / Allen, A. / Sum, M. / Obier, N. / Cottard, F. / Ulferts, S. / Preca, B.T. / Hermann, B. / Maurer, J. / ...Authors: Metzger, E. / Wang, S. / Urban, S. / Willmann, D. / Schmidt, A. / Offermann, A. / Allen, A. / Sum, M. / Obier, N. / Cottard, F. / Ulferts, S. / Preca, B.T. / Hermann, B. / Maurer, J. / Greschik, H. / Hornung, V. / Einsle, O. / Perner, S. / Imhof, A. / Jung, M. / Schule, R.
History
DepositionApr 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Database references / Source and taxonomy / Category: entity_src_gen / struct_ref / struct_ref_seq
Item: _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id ..._entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidoglycan D,D-transpeptidase MrdA


Theoretical massNumber of molelcules
Total (without water)65,0761
Polymers65,0761
Non-polymers00
Water6,467359
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 area24130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.190, 182.064, 75.362
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-702-

HOH

21A-705-

HOH

31A-839-

HOH

41A-912-

HOH

51A-1049-

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: PBP2 Eco Apo (50-637) from limited proteolysis by Endoproteinase GluC
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: mrdA, pbpA, b0635, JW0630 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P0AD65, serine-type D-Ala-D-Ala carboxypeptidase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 359 / Source method: isolated from a natural source / Formula: H2O

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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: 3.3 Å3/Da / Density % sol: 62.72 %
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: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.5418 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Nov 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→45.52 Å / Num. obs: 50209 / % possible obs: 98.31 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 7.92
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4.9 % / Num. unique obs: 4904 / % possible all: 88

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6G9S

6g9s


Resolution: 2.101→45.516 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.21
RfactorNum. reflection% reflection
Rfree0.2357 3728 3.97 %
Rwork0.1993 --
obs0.2008 49696 96.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.101→45.516 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4254 0 0 359 4613
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074360
X-RAY DIFFRACTIONf_angle_d0.8985927
X-RAY DIFFRACTIONf_dihedral_angle_d3.1382603
X-RAY DIFFRACTIONf_chiral_restr0.051641
X-RAY DIFFRACTIONf_plane_restr0.006770
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1006-2.12720.4012840.41731912X-RAY DIFFRACTION55
2.1272-2.15510.45281150.37853110X-RAY DIFFRACTION88
2.1551-2.18470.44291350.36463125X-RAY DIFFRACTION93
2.1847-2.21590.37641290.363292X-RAY DIFFRACTION94
2.2159-2.2490.35741390.32993302X-RAY DIFFRACTION96
2.249-2.28410.321370.33663335X-RAY DIFFRACTION97
2.2841-2.32150.36481350.32233360X-RAY DIFFRACTION98
2.3215-2.36160.33161440.31553451X-RAY DIFFRACTION98
2.3616-2.40450.35741360.29353362X-RAY DIFFRACTION99
2.4045-2.45080.29131390.27643457X-RAY DIFFRACTION99
2.4508-2.50080.2791400.27143429X-RAY DIFFRACTION100
2.5008-2.55510.3491460.273441X-RAY DIFFRACTION100
2.5551-2.61460.29481450.26623458X-RAY DIFFRACTION100
2.6146-2.680.29031440.25043464X-RAY DIFFRACTION100
2.68-2.75240.34031390.2433423X-RAY DIFFRACTION100
2.7524-2.83340.24621450.24093468X-RAY DIFFRACTION100
2.8334-2.92480.26781460.22293449X-RAY DIFFRACTION100
2.9248-3.02930.29981440.21543463X-RAY DIFFRACTION100
3.0293-3.15060.26421450.21133449X-RAY DIFFRACTION100
3.1506-3.2940.27671410.19443405X-RAY DIFFRACTION100
3.294-3.46760.19481400.18163448X-RAY DIFFRACTION100
3.4676-3.68470.21611500.16333438X-RAY DIFFRACTION100
3.6847-3.96910.20921420.14833468X-RAY DIFFRACTION100
3.9691-4.36820.14011410.13363420X-RAY DIFFRACTION100
4.3682-4.99960.16521430.12743384X-RAY DIFFRACTION98
4.9996-6.29630.1941420.16243403X-RAY DIFFRACTION98
6.2963-45.52670.18751420.17163412X-RAY DIFFRACTION99

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