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Open data
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Basic information
Entry | Database: PDB / ID: 6g3d | ||||||
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Title | Crystal structure of Native EDDS lyase | ||||||
![]() | Argininosuccinate lyase | ||||||
![]() | LYASE / C-N Lyase / metal chelator / EDDS / tetramer / aspartase fumarase superfamily | ||||||
Function / homology | ![]() argininosuccinate lyase / argininosuccinate lyase activity / arginine biosynthetic process via ornithine / cytosol Similarity search - Function | ||||||
Biological species | Chelativorans sp. | ||||||
Method | ![]() ![]() | ||||||
![]() | Poddar, H. / Thunnissem, A.M.W.H. / Poelarends, G.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Basis for the Catalytic Mechanism of Ethylenediamine- N, N'-disuccinic Acid Lyase, a Carbon-Nitrogen Bond-Forming Enzyme with a Broad Substrate Scope. Authors: Poddar, H. / de Villiers, J. / Zhang, J. / Puthan Veetil, V. / Raj, H. / Thunnissen, A.W.H. / Poelarends, G.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 113 KB | Display | ![]() |
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PDB format | ![]() | 86.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 418.3 KB | Display | ![]() |
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Full document | ![]() | 420 KB | Display | |
Data in XML | ![]() | 20.3 KB | Display | |
Data in CIF | ![]() | 29.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6g3eC ![]() 6g3fC ![]() 6g3gC ![]() 6g3hC ![]() 6g3iC ![]() 1tjuS ![]() 1u15S ![]() 2e9fS 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 55758.246 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: BNC1 / Gene: Meso_0564 / Plasmid: pBADN / Production host: ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.46 Å3/Da / Density % sol: 64.44 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5 and 4 M NaCl |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 11, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.22→51.7 Å / Num. obs: 37577 / % possible obs: 98.5 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.151 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2.22→2.27 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.544 / Mean I/σ(I) obs: 2.8 / % possible all: 94.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1TJU,2E9F,1U15 Resolution: 2.221→51.679 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.86
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.221→51.679 Å
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Refine LS restraints |
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LS refinement shell |
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