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- PDB-7e61: The crystal structure of peptidoglycan peptidase in complex with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7.0E+61 | ||||||
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Title | The crystal structure of peptidoglycan peptidase in complex with inhibitor 2 | ||||||
![]() | Peptidase M23 | ||||||
![]() | HYDROLASE/INHIBITOR / HYDROLASE-INHIBITOR COMPLEX | ||||||
Function / homology | Peptidase M23 / Peptidase family M23 / Duplicated hybrid motif / Chem-HXF / Peptidase M23![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Min, K.J. / Yoon, H.J. / Choi, Y. / Lee, H.H. | ||||||
![]() | ![]() Title: Structure-based inhibitor design for reshaping bacterial morphology Authors: Choi, Y. / Park, J.S. / Kim, J. / Min, K. / Mahasenan, K. / Kim, C. / Yoon, H.J. / Lim, S. / Cheon, D.H. / Lee, Y. / Ryu, S. / Mobashery, S. / Kim, B.M. / Lee, H.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 73.7 KB | Display | ![]() |
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PDB format | ![]() | 52 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 15.1 KB | Display | |
Data in CIF | ![]() | 22 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7e60C ![]() 7e63C ![]() 7e64C ![]() 7e65C ![]() 7e66C ![]() 7e67C ![]() 7e69C ![]() 6jmzS 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 28463.752 Da / Num. of mol.: 1 / Mutation: H247A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-HXF / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.72 Å3/Da / Density % sol: 66.96 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop Details: 0.1 M sodium acetate: acetic acid pH 4.5 and 0.8 M NaH2PO4/1.2 M K2HPO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 14, 2020 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→48.403 Å / Num. obs: 38961 / % possible obs: 100 % / Redundancy: 10.595 % / Biso Wilson estimate: 35.238 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.048 / Rrim(I) all: 0.051 / Χ2: 0.952 / Net I/σ(I): 29.48 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6JMZ Resolution: 1.8→48.403 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.574 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 104.2 Å2 / Biso mean: 34.931 Å2 / Biso min: 17.92 Å2
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Refinement step | Cycle: final / Resolution: 1.8→48.403 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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