+Open data
-Basic information
Entry | Database: PDB / ID: 8wt4 | ||||||
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Title | Crystal structure of DL-endopeptidase CwlO complexed with IseA | ||||||
Components |
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Keywords | HYDROLASE / Peptidoglycan DL-endopeptidase / autolysin / a complex of DL-endopeptidase and inhibitory protein | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases) / cysteine-type peptidase activity / cell wall organization / proteolysis / extracellular region Similarity search - Function | ||||||
Biological species | Bacillus subtilis subsp. subtilis str. 168 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å | ||||||
Authors | Tandukar, S. / Kwon, E. / Kim, D.Y. | ||||||
Funding support | 1items
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Citation | Journal: Febs J. / Year: 2024 Title: Structural analysis of the peptidoglycan DL-endopeptidase CwlO complexed with its inhibitory protein IseA. Authors: Tandukar, S. / Kwon, E. / Kim, D.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8wt4.cif.gz | 85.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8wt4.ent.gz | 61.1 KB | Display | PDB format |
PDBx/mmJSON format | 8wt4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8wt4_validation.pdf.gz | 423.2 KB | Display | wwPDB validaton report |
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Full document | 8wt4_full_validation.pdf.gz | 423.5 KB | Display | |
Data in XML | 8wt4_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | 8wt4_validation.cif.gz | 29.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wt/8wt4 ftp://data.pdbj.org/pub/pdb/validation_reports/wt/8wt4 | HTTPS FTP |
-Related structure data
Related structure data | 8wt3C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20168.461 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria) Gene: yoeB, BSU18380 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O34841 |
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#2: Protein | Mass: 14176.695 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria) Gene: cwlO, yvcE, yzkA, BSU34800 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P40767, Hydrolases; Acting on peptide bonds (peptidases) |
#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: 2.74 Å3/Da / Density % sol: 55.11 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 7.5 Details: 30% (v/v) isopropanol, 15% (v/v) PEG 3350, 0.2 M ammonium citrate/citric acid pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 13, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→92.2 Å / Num. obs: 47169 / % possible obs: 96.9 % / Redundancy: 4.22 % / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.046 / Rrim(I) all: 0.096 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.62→1.65 Å / Redundancy: 4.25 % / Rmerge(I) obs: 0.759 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2375 / Rpim(I) all: 0.41 / Rrim(I) all: 0.826 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.62→55.44 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.53 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.92 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.62→55.44 Å
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Refine LS restraints |
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LS refinement shell |
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