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Open data
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Basic information
Entry | Database: PDB / ID: 7v6u | ||||||
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Title | Crystal structure of bacterial peptidase | ||||||
![]() | Murein DD-endopeptidase MepS/Murein LD-carboxypeptidase | ||||||
![]() | HYDROLASE / NlpC/P60 | ||||||
Function / homology | ![]() muramoyltetrapeptide carboxypeptidase / muramoyltetrapeptide carboxypeptidase activity / capsule polysaccharide biosynthetic process / peptidoglycan metabolic process / peptidoglycan turnover / Hydrolases; Acting on peptide bonds (peptidases) / cysteine-type peptidase activity / cell wall organization / cell outer membrane / endopeptidase activity / proteolysis Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kim, Y. / Lee, W.C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The crystal structure of bacterial DD-endopeptidase Authors: Lee, W.C. / Lee, J. / Kim, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 63.9 KB | Display | ![]() |
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PDB format | ![]() | 46.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.7 KB | Display | ![]() |
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Full document | ![]() | 457.6 KB | Display | |
Data in XML | ![]() | 11.5 KB | Display | |
Data in CIF | ![]() | 14.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2k1gS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15035.954 Da / Num. of mol.: 2 / Mutation: C68S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: mepS, spr, yeiV, b2175, JW2163 / Plasmid: pET28a / Production host: ![]() ![]() References: UniProt: P0AFV4, muramoyltetrapeptide carboxypeptidase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.87 % |
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Crystal grow | Temperature: 290 K / Method: evaporation / pH: 7 / Details: 0.2M DL-Malic acid, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 22, 2020 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.14→41.432 Å / Num. obs: 13739 / % possible obs: 95 % / Redundancy: 3.563 % / Biso Wilson estimate: 26.92 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.103 / Rrim(I) all: 0.122 / Χ2: 0.85 / Net I/σ(I): 9.86 / Num. measured all: 48953 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2K1G Resolution: 2.144→41.432 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.02 / 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 max: 80.27 Å2 / Biso mean: 30.3903 Å2 / Biso min: 11.62 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.144→41.432 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19
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