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- PDB-2r8w: The crystal structure of dihydrodipicolinate synthase (Atu0899) f... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2r8w | ||||||
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Title | The crystal structure of dihydrodipicolinate synthase (Atu0899) from Agrobacterium tumefaciens str. C58 | ||||||
![]() | AGR_C_1641p | ||||||
![]() | LYASE / APC7498 / Dihydrodipicolinate synthase / Agrobacterium tumefaciens str. C58 / structural genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tan, K. / Dong, A. / Xu, X. / Gu, J. / Zheng, H. / Edwards, A.M. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
![]() | ![]() Title: The crystal structure of dihydrodipicolinate synthase (Atu0899) from Agrobacterium tumefaciens str. C58. Authors: Tan, K. / Dong, A. / Xu, X. / Gu, J. / Zheng, H. / Edwards, A.M. / Savchenko, A. / Joachimiak, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 133.8 KB | Display | ![]() |
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PDB format | ![]() | 109.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.9 KB | Display | ![]() |
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Full document | ![]() | 453.4 KB | Display | |
Data in XML | ![]() | 28 KB | Display | |
Data in CIF | ![]() | 42.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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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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Details | Authors state that the biological unit is experimentally unknown. From molecular packing, it is likely a dimer formed from chains A and B that are present in the asymmetric unit. |
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Components
#1: Protein | Mass: 36141.914 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Species: Agrobacterium tumefaciens / Strain: C58 / Gene: AGR_C_1641 / Plasmid: pET derivative / Species (production host): Escherichia coli / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.18 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1M Tris-HCl pH 8.5, 0.2M Na(OAC), 30% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 28, 2007 / Details: mirrors |
Radiation | Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→43.52 Å / Num. all: 49541 / Num. obs: 49541 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.5 % / Biso Wilson estimate: 19.3 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 31.9 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.534 / Mean I/σ(I) obs: 5 / Num. unique all: 4915 / % possible all: 98.4 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 18.511 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→43.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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