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- PDB-2dbi: Crystal Structure of a Hypothetical Protein JW0805 from Escherich... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2dbi | ||||||
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Title | Crystal Structure of a Hypothetical Protein JW0805 from Escherichia coli | ||||||
![]() | Hypothetical protein ybiU | ||||||
![]() | Structural genomics / unknown function / alpha/beta structure / hypothetical protein / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Gig2-like / Gig2-like / B-lactam Antibiotic, Isopenicillin N Synthase; Chain / Isopenicillin N synthase-like superfamily / Jelly Rolls / Sandwich / Mainly Beta / Uncharacterized protein YbiU![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ihsanawati / Murayama, K. / Bessho, Y. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() Title: Crystal Structure of a Hypothetical Protein JW0805 from Escherichia coli Authors: Ihsanawati / Murayama, K. / Bessho, Y. / Shirouzu, M. / Yokoyama, 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 | ![]() | 107.2 KB | Display | ![]() |
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PDB format | ![]() | 79.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 417.8 KB | Display | ![]() |
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Full document | ![]() | 420.6 KB | Display | |
Data in XML | ![]() | 22.1 KB | Display | |
Data in CIF | ![]() | 35.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2dbnS S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 51920.113 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: 2.38 Å3/Da / Density % sol: 48.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1M bis-tris pH5.5, 25% PEG 3350, 0.2M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Jul 20, 2005 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 32097 / % possible obs: 93.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 6.2 Å2 |
Reflection shell | Resolution: 2→2.07 Å / % possible all: 36.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2DBN Resolution: 2.05→30 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3570523.67 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 56.7085 Å2 / ksol: 0.362091 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 17.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.05→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.07→2.13 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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