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Yorodumi- PDB-7e67: The crystal structure of peptidoglycan peptidase in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7.0E+67 | ||||||
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Title | The crystal structure of peptidoglycan peptidase in complex with inhibitor 3-2 | ||||||
Components | Peptidase M23 | ||||||
Keywords | HYDROLASE/INHIBITOR / HYDROLASE-INHIBITOR COMPLEX | ||||||
Function / homology | Peptidase M23 / Peptidase family M23 / Duplicated hybrid motif / Chem-HXR / Peptidase M23 Function and homology information | ||||||
Biological species | Campylobacter jejuni (Campylobacter) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | ||||||
Authors | Choi, Y. / Min, K.J. / Yoon, H.J. / Lee, H.H. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Commun Biol / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7e67.cif.gz | 66.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7e67.ent.gz | 46.6 KB | Display | PDB format |
PDBx/mmJSON format | 7e67.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7e67_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7e67_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7e67_validation.xml.gz | 11.3 KB | Display | |
Data in CIF | 7e67_validation.cif.gz | 14.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e6/7e67 ftp://data.pdbj.org/pub/pdb/validation_reports/e6/7e67 | HTTPS FTP |
-Related structure data
Related structure data | 7e60C 7e61C 7e63C 7e64C 7e65C 7e66C 7e69C 6jmzS C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 28463.752 Da / Num. of mol.: 1 / Mutation: H247A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: A8118_01115 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1J6PWI8 |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-HXR / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.81 Å3/Da / Density % sol: 67.7 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop Details: 0.2 M ammonium sulfate, 0.1 M sodium acetate trihydrate pH 4.6, and 30 % Polyethylene glycol monomethyl ether 2,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 25, 2020 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.85→49.24 Å / Num. obs: 19590 / % possible obs: 100 % / Redundancy: 10.612 % / Biso Wilson estimate: 46.878 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.201 / Rrim(I) all: 0.212 / Χ2: 0.841 / Net I/σ(I): 11.33 / Num. measured all: 207883 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6JMZ Resolution: 2.85→49.24 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.882 / SU B: 14.35 / SU ML: 0.276 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.777 / ESU R Free: 0.372 / 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: 106.17 Å2 / Biso mean: 48.711 Å2 / Biso min: 17.2 Å2
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Refinement step | Cycle: final / Resolution: 2.85→49.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.85→2.924 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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