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- PDB-3r79: Crystal structure of an uncharactertized protein from Agrobacteri... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3r79 | ||||||
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Title | Crystal structure of an uncharactertized protein from Agrobacterium tumefaciens | ||||||
![]() | uncharacterized protein | ||||||
![]() | Structure Genomics / unknown function / PSI-biology / Structural Genomics / New York Structural Genomics Research Consortium / TIM barrel / alanine racemase / YBL036c-like proteins / pyridoxal 5' phosphate / metal ion / NYSGRC | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Eswaramoorthy, S. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC) | ||||||
![]() | ![]() Title: Crystal structure of an uncharactertized protein from Agrobacterium tumefaciens Authors: Eswaramoorthy, S. / Almo, S.C. / Swaminathan, 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 | ![]() | 98.2 KB | Display | ![]() |
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PDB format | ![]() | 79.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 466.2 KB | Display | ![]() |
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Full document | ![]() | 468.4 KB | Display | |
Data in XML | ![]() | 19 KB | Display | |
Data in CIF | ![]() | 26.9 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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2 | ![]()
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3 | ![]()
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Unit cell |
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Details | monomer |
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Components
#1: Protein | Mass: 27127.004 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-ACT / | #4: Chemical | ChemComp-PLP / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 20% PEG 8000; 0.1M Na Cacodylate ph 6.5; 0.2M Mg Acetate; Praseodymium (III) Acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 4, 2010 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 41253 / Num. obs: 41253 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.4 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 1.9→1.96 Å / Redundancy: 14.6 % / Rmerge(I) obs: 0.487 / Num. unique all: 3395 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 19 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.014
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