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- PDB-2i3o: Crystal structure of gamma-glutamyl transferase related protein f... -
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Basic information
Entry | Database: PDB / ID: 2i3o | ||||||
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Title | Crystal structure of gamma-glutamyl transferase related protein from Thermoplasma acidophilum | ||||||
![]() | Gamma-glutamyltransferase related protein | ||||||
![]() | TRANSFERASE / Gamma-glutamyl transferase related protein / Thermoplasma acidophilum / 6324d / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Gamma-glutamyltranspeptidase / Gamma-glutamyltranspeptidase, small subunit / Nucleophile aminohydrolases, N-terminal / transferase activity / Gamma-glutamyltransferase related protein![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rao, K.N. / Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
![]() | ![]() Title: Crystal structure of gamma-glutamyl transferase related protein from Thermoplasma acidophilum Authors: Rao, K.N. / Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 398.4 KB | Display | ![]() |
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PDB format | ![]() | 337.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 459.4 KB | Display | ![]() |
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Full document | ![]() | 488.4 KB | Display | |
Data in XML | ![]() | 78.7 KB | Display | |
Data in CIF | ![]() | 110.2 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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Unit cell |
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Components
#1: Protein | Mass: 57578.977 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.34 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: Magnesium Formate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 14, 2006 / Details: Mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→50 Å / Num. all: 156657 / Num. obs: 156657 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 11.4 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2.03→2.1 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 3 / Num. unique all: 15286 / Rsym value: 0.38 / % possible all: 97.9 |
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Processing
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Refinement | Method to determine structure: ![]() Details: Residues listed in remark 465 and atoms listed in remark 470 were not modeled due to lack of electron density. Residue ASN254 in all four chains does not have good geometry. However, they ...Details: Residues listed in remark 465 and atoms listed in remark 470 were not modeled due to lack of electron density. Residue ASN254 in all four chains does not have good geometry. However, they fit the electron density very well. Residual densities near the active sites have been modeled as water (39, 40, 45, 167) but they could be metal ions. N terminal Selenomethionine is visible only in chains A and D.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.6224 Å2 / ksol: 0.369856 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.03→30.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.03→2.16 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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