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Open data
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Basic information
Entry | Database: PDB / ID: 6g9p | ||||||
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Title | Structural basis for the inhibition of E. coli PBP2 | ||||||
![]() | Peptidoglycan D,D-transpeptidase MrdA | ||||||
![]() | HYDROLASE/ANTIBIOTIC / penicillin binding protein / HYDROLASE-ANTIBIOTIC COMPLEX | ||||||
Function / homology | ![]() 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 | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Ruff, M. / Levy, N. | ||||||
![]() | ![]() 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: ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 130.4 KB | Display | ![]() |
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PDB format | ![]() | 98.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6g9fC ![]() 6g9sSC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | 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.) ![]() ![]() ![]() ![]() References: UniProt: P0AD65, serine-type D-Ala-D-Ala carboxypeptidase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 62.72 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Nov 8, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 2.1→2.18 Å / Redundancy: 4.9 % / Num. unique obs: 4904 / % possible all: 88 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.101→45.516 Å
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Refine LS restraints |
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LS refinement shell |
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