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- PDB-3p51: Three-dimensional structure of protein Q2Y8N9_NITMU from nitrosos... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3p51 | ||||||
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Title | Three-dimensional structure of protein Q2Y8N9_NITMU from nitrosospira multiformis, Northeast structural genomics consortium target NMR118 | ||||||
![]() | Uncharacterized protein | ||||||
![]() | Structural genomics / Unknown function / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Polyketide cyclase/dehydrase / Polyketide cyclase / dehydrase and lipid transport / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta / Polyketide cyclase / dehydrase and lipid transport![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kuzin, A. / Chen, Y. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. ...Kuzin, A. / Chen, Y. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
![]() | ![]() Title: Northeast Structural Genomics Consortium Target NmR118 Authors: Kuzin, A. / Chen, Y. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 72.9 KB | Display | ![]() |
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PDB format | ![]() | 58.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 419.7 KB | Display | ![]() |
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Full document | ![]() | 420.8 KB | Display | |
Data in XML | ![]() | 9.1 KB | Display | |
Data in CIF | ![]() | 12.5 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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Components on special symmetry positions |
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Components
#1: Protein | Mass: 18417.891 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.15 % |
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Crystal grow | Temperature: 293 K / Method: macrobatch under oil / pH: 7 Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), Reservoir solution: LiCl 4.42M, Bis-Tris Propane 0.1M, macrobatch under oil, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 1, 2010 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. obs: 23884 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 10.7 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 39.5 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.9 / % possible all: 83.3 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.95 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.833 Å2 / ksol: 0.351 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 128.04 Å2 / Biso mean: 45.23 Å2 / Biso min: 24.32 Å2
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Refinement step | Cycle: LAST / Resolution: 2.056→40.204 Å
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Refinement TLS params. | Method: refined / Origin x: 24.9863 Å / Origin y: 18.729 Å / Origin z: 63.3293 Å
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Refinement TLS group | Selection details: all |