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- PDB-5ygr: Crystal structure of PLP bound Diaminopropionate ammonia lyase fr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ygr | ||||||
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Title | Crystal structure of PLP bound Diaminopropionate ammonia lyase from Salmonella typhimurium | ||||||
![]() | (Diaminopropionate ammonia ...) x 2 | ||||||
![]() | LYASE / dimer / internal aldimine | ||||||
Function / homology | ![]() diaminopropionate ammonia-lyase / diaminopropionate ammonia-lyase activity / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Geeta, D. / Shveta, B. / Shavithri, H.S. / Murthy, M.R.N. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Comparative structural and enzymatic studies on Salmonella typhimurium diaminopropionate ammonia lyase reveal its unique features Authors: Deka, G. / Bisht, S. / Savithri, H.S. / Murthy, M.R.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 308 KB | Display | ![]() |
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PDB format | ![]() | 241.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 506.6 KB | Display | ![]() |
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Full document | ![]() | 531.4 KB | Display | |
Data in XML | ![]() | 63.8 KB | Display | |
Data in CIF | ![]() | 87.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4d9gS 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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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: GLN / Beg label comp-ID: GLN / Refine code: _
NCS ensembles :
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Components
-Diaminopropionate ammonia ... , 2 types, 4 molecules ABCD
#1: Protein | Mass: 44426.301 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: LT2 / Gene: ygeX / Plasmid: pET22b / Production host: ![]() ![]() References: UniProt: P40817*PLUS, diaminopropionate ammonia-lyase |
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#2: Protein | Mass: 45497.441 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: LT2 / Gene: ygeX / Plasmid: pET22b / Production host: ![]() ![]() References: UniProt: P40817*PLUS, diaminopropionate ammonia-lyase |
-Non-polymers , 4 types, 603 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-EDO / #4: Chemical | #5: Chemical | ChemComp-PO4 / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.45 % / Description: Thin plate like crystals |
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Crystal grow | Temperature: 298 K / Method: microbatch / pH: 5.6 Details: 20%(w/v) PEG4000, 20%(v/v) 2-propanol, 100mM sodium citrate pH 5.6, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 25, 2014 |
Radiation | Monochromator: Si(III) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.956 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→77.16 Å / Num. obs: 58141 / % possible obs: 99.9 % / Redundancy: 4.6 % / Biso Wilson estimate: 28.2 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.07 / Rsym value: 0.15 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 8417 / CC1/2: 0.83 / Rpim(I) all: 0.33 / Rsym value: 0.73 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4D9G Resolution: 2.5→77 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.871 / SU B: 13.51 / SU ML: 0.296 / Cross valid method: THROUGHOUT / ESU R: 0.705 / ESU R Free: 0.35 / 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: 43.533 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→77 Å
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Refine LS restraints |
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