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- PDB-5fag: Alanine Racemase from Streptomyces coelicolor A3(2) with Bound Pr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5fag | ||||||
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Title | Alanine Racemase from Streptomyces coelicolor A3(2) with Bound Propionate Inhibitor | ||||||
![]() | Alanine racemase | ||||||
![]() | ISOMERASE / PLP / alanine racemase / propionate | ||||||
Function / homology | ![]() alanine racemase / D-alanine biosynthetic process / alanine racemase activity / peptidoglycan biosynthetic process / pyridoxal phosphate binding / cytosol Similarity search - Function | ||||||
Biological species | Streptomyces coelicolor A3 | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tassoni, R. / Pannu, N.S. | ||||||
![]() | ![]() Title: Structural and functional characterization of the alanine racemase from Streptomyces coelicolor A3(2). Authors: Tassoni, R. / van der Aart, L.T. / Ubbink, M. / van Wezel, G.P. / Pannu, N.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 323.8 KB | Display | ![]() |
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PDB format | ![]() | 259.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 514.7 KB | Display | ![]() |
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Full document | ![]() | 538.2 KB | Display | |
Data in XML | ![]() | 66.1 KB | Display | |
Data in CIF | ![]() | 93.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5facSC ![]() 5fajC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / Refine code: _
NCS ensembles :
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 43373.941 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: alr, SCO4745, SC6G4.23 / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 823 molecules ![](data/chem/img/PLP.gif)
![](data/chem/img/PPI.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/NO3.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PPI.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/NO3.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-PLP / #3: Chemical | ChemComp-PPI / #4: Chemical | ChemComp-NA / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.28 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 0.1 M BIS-TRIS propane pH 8.5, 0.2 M NaNO3, 20% (w/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 2, 2015 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.968622 Å / Relative weight: 1 |
Reflection | Resolution: 1.51→48.06 Å / Num. obs: 224162 / % possible obs: 96.8 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 1.51→1.56 Å / Redundancy: 2.2 % / Rmerge(I) obs: 1.016 / Mean I/σ(I) obs: 0.8 / % possible all: 90.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5FAC Resolution: 1.51→48.06 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.783 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.274 Å2
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Refinement step | Cycle: 1 / Resolution: 1.51→48.06 Å
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Refine LS restraints |
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