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Open data
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Basic information
Entry | Database: PDB / ID: 8c0j | ||||||
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Title | Structure of AmiB enzymatic domain bound to the EnvC LytM domain | ||||||
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![]() | HYDROLASE / Complex | ||||||
Function / homology | ![]() N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan catabolic process / hydrolase activity Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Crow, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Activator-induced conformational changes regulate division-associated peptidoglycan amidases. Authors: Cook, J. / Baverstock, T.C. / McAndrew, M.B.L. / Roper, D.I. / Stansfeld, P.J. / Crow, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 121.9 KB | Display | ![]() |
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PDB format | ![]() | 90.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 869.2 KB | Display | ![]() |
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Full document | ![]() | 882.7 KB | Display | |
Data in XML | ![]() | 21.1 KB | Display | |
Data in CIF | ![]() | 28.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8c2oC C: citing same article ( |
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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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: LEU / End label comp-ID: LEU / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 190 - 421 / Label seq-ID: 2 - 233
NCS ensembles : (Details: Local NCS retraints between domains: 1 2) |
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Components
#1: Protein | Mass: 25585.688 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A0A482PQR2, N-acetylmuramoyl-L-alanine amidase #2: Protein | | Mass: 16141.135 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | #4: Chemical | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.14 Å3/Da / Density % sol: 70.28 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: Na Phosphate pH7.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 11, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95373 Å / Relative weight: 1 |
Reflection | Resolution: 3.38→59.34 Å / Num. obs: 16294 / % possible obs: 100 % / Redundancy: 78.2 % / Biso Wilson estimate: 81 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.088 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 3.38→3.65 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3305 / CC1/2: 0.939 / Rpim(I) all: 0.686 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: in silico model Resolution: 3.381→50.005 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.878 / SU B: 26.314 / SU ML: 0.383 / Cross valid method: FREE R-VALUE / ESU R Free: 0.517 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 119.898 Å2
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Refinement step | Cycle: LAST / Resolution: 3.381→50.005 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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