+Open data
-Basic information
Entry | Database: PDB / ID: 6g3e | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of EDDS lyase in complex with formate | ||||||
Components | Argininosuccinate lyase | ||||||
Keywords | LYASE / C-N Lyase / metal chelator / EDDS / formate / tetramer / aspartase fumarase superfamily | ||||||
Function / homology | Function and homology information argininosuccinate lyase / argininosuccinate lyase activity / arginine biosynthetic process via ornithine / cytosol Similarity search - Function | ||||||
Biological species | Chelativorans sp. | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Poddar, H. / Thunnissem, A.M.W.H. / Poelarends, G.J. | ||||||
Funding support | Netherlands, 1items
| ||||||
Citation | Journal: Biochemistry / Year: 2018 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6g3e.cif.gz | 119.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6g3e.ent.gz | 90 KB | Display | PDB format |
PDBx/mmJSON format | 6g3e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6g3e_validation.pdf.gz | 431.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6g3e_full_validation.pdf.gz | 431.7 KB | Display | |
Data in XML | 6g3e_validation.xml.gz | 22.5 KB | Display | |
Data in CIF | 6g3e_validation.cif.gz | 34.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g3/6g3e ftp://data.pdbj.org/pub/pdb/validation_reports/g3/6g3e | HTTPS FTP |
-Related structure data
Related structure data | 6g3dSC 6g3fC 6g3gC 6g3hC 6g3iC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 55758.246 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chelativorans sp. (strain BNC1) (bacteria) Strain: BNC1 / Gene: Meso_0564 / Plasmid: pBADN / Production host: Escherichia coli (E. coli) / References: UniProt: Q11KV9 | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.38 Å3/Da / Density % sol: 63.65 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M sodium cacodylate pH 6.5 and 2.0 M sodium formate |
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 3, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→41.7 Å / Num. obs: 58476 / % possible obs: 99.3 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.6 / % possible all: 97.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6G3D Resolution: 1.9→19.991 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 14.64
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→19.991 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|