+Open data
-Basic information
Entry | Database: PDB / ID: 6g9f | ||||||
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Title | Structural basis for the inhibition of E. coli PBP2 | ||||||
Components | Peptidoglycan D,D-transpeptidase MrdA | ||||||
Keywords | HYDROLASE/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 | ||||||
Biological species | Escherichia coli K-12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Ruff, 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6g9f.cif.gz | 232.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6g9f.ent.gz | 187.5 KB | Display | PDB format |
PDBx/mmJSON format | 6g9f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6g9f_validation.pdf.gz | 751.8 KB | Display | wwPDB validaton report |
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Full document | 6g9f_full_validation.pdf.gz | 758.9 KB | Display | |
Data in XML | 6g9f_validation.xml.gz | 22.1 KB | Display | |
Data in CIF | 6g9f_validation.cif.gz | 30.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g9/6g9f ftp://data.pdbj.org/pub/pdb/validation_reports/g9/6g9f | HTTPS FTP |
-Related structure data
Related structure data | 6g9pC 6g9sSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 62809.215 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The Ser 330 in the structure is modified covalently and is named (S31) 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 |
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#2: Chemical | ChemComp-NXL / ( |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.38 Å3/Da / Density % sol: 63.56 % |
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Crystal grow | Temperature: 300 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] equilibrated against 2.0 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.5418 Å |
Detector | Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Feb 8, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→39.005 Å / Num. obs: 35810 / % possible obs: 98.67 % / Redundancy: 5.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.1454 / Rpim(I) all: 0.06713 / Rrim(I) all: 0.1607 / Net I/σ(I): 7.87 |
Reflection shell | Resolution: 2.35→2.434 Å / Redundancy: 5.6 % / Rmerge(I) obs: 2.546 / Num. unique obs: 3525 / CC1/2: 0.419 / Rpim(I) all: 1.167 / Rrim(I) all: 2.809 / % possible all: 95.57 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6G9S Resolution: 2.35→39.01 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.04
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→39.01 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 28.995 Å / Origin y: 55.231 Å / Origin z: 38.5428 Å
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Refinement TLS group | Selection details: ALL |