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- PDB-5ls7: Complex of wild type E. coli alpha aspartate decarboxylase with i... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ls7 | |||||||||||||||
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Title | Complex of wild type E. coli alpha aspartate decarboxylase with its processing factor PanZ | |||||||||||||||
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![]() | LYASE / protein derived cofactor / coenzyme A biosynthesis / protein complex / metabolic pathway regulation | |||||||||||||||
Function / homology | ![]() alanine biosynthetic process / aspartate 1-decarboxylase / aspartate 1-decarboxylase activity / acetyl-CoA binding / pantothenate biosynthetic process / zymogen activation / acyltransferase activity, transferring groups other than amino-acyl groups / protein autoprocessing / protein processing / cytosol Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Monteiro, D.C.F. / Webb, M.E. / Pearson, A.R. | |||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: The Mechanism of Regulation of Pantothenate Biosynthesis by the PanD-PanZAcCoA Complex Reveals an Additional Mode of Action for the Antimetabolite N-Pentyl Pantothenamide (N5-Pan). Authors: Arnott, Z.L.P. / Nozaki, S. / Monteiro, D.C.F. / Morgan, H.E. / Pearson, A.R. / Niki, H. / Webb, M.E. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 137 KB | Display | ![]() |
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PDB format | ![]() | 103.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 720.1 KB | Display | ![]() |
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Full document | ![]() | 733.5 KB | Display | |
Data in XML | ![]() | 18.9 KB | Display | |
Data in CIF | ![]() | 26.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4cryS 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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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
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Components
-Protein/peptide , 1 types, 1 molecules A
#1: Protein/peptide | Mass: 4770.559 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Residues 1-17 are the purification tag. / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Protein , 2 types, 2 molecules BD
#2: Protein | Mass: 15738.804 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The C-terminus is not visible in the electron density Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#3: Protein | Mass: 11044.332 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The N-terminal residue is a pyruvoyl moiety formed after post-translation backbone cleavage after protein folding. Cysteine 78 is oxidised. Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Non-polymers , 8 types, 304 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/ACO.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CO2.gif)
![](data/chem/img/SCN.gif)
![](data/chem/img/74C.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/ACO.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CO2.gif)
![](data/chem/img/SCN.gif)
![](data/chem/img/74C.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-ACO / | #7: Chemical | ChemComp-MG / | #8: Chemical | #9: Chemical | #10: Chemical | ChemComp-74C / | #11: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | CO2 derives from the sidechains of GLU B 70 and D 113 which have decomposed due to radiation damage. ...CO2 derives from the sidechains of GLU B 70 and D 113 which have decomposed due to radiation damage. 74C methyl radical derives from MET D114 as a result of radiation damage |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.01 % / Description: Bipyrimidal |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 200 mM KSCN, 100 mM Bis-Tris propane pH 6.5, 20% v/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 6, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.16→29.28 Å / Num. obs: 99822 / % possible obs: 99.6 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 9 |
Reflection shell | Resolution: 1.16→1.18 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 2.1 / % possible all: 93.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4CRY Resolution: 1.16→29.28 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.98 / SU B: 0.992 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.026 / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.859 Å2
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Refinement step | Cycle: LAST / Resolution: 1.16→29.28 Å
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Refine LS restraints |
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