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- PDB-1y23: Crystal structure of a member of HIT family of proteins from baci... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1y23 | ||||||
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Title | Crystal structure of a member of HIT family of proteins from bacillus subtilis | ||||||
![]() | Histidine triad protein | ||||||
![]() | CELL CYCLE / HIT protein / PKCI-1 / cell-cycle regulation / histidine triad / NYSGXRC / Structural Genomics / Protein Structure Initiative / T2097 / New York SGX Research Center for Structural Genomics / PSI | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rajashankar, K.R. / Lima, C.D. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
![]() | ![]() Title: Crystal structure of a member of HIT family of proteins from bacillus subtilis Authors: Rajashankar, K.R. / Lima, C.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 153.6 KB | Display | ![]() |
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PDB format | ![]() | 122.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.5 KB | Display | ![]() |
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Full document | ![]() | 468.4 KB | Display | |
Data in XML | ![]() | 29.9 KB | Display | |
Data in CIF | ![]() | 41.7 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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Components on special symmetry positions |
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Details | Biological molecule is a dimer. Protomers A and B together form one biological assembly and so do protomers C and D. The partner protomer for molecule E is generated by the crystallographic two fold operation x, -y, -z+2/3 |
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Components
#1: Protein | Mass: 16322.483 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-MG / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 47.98 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 19.5% Peg 4000, 0.5M Ammonium Acetate, 0.1M Sodium Citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→19.96 Å / Num. all: 35084 / Num. obs: 35084 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 17.5 % / Biso Wilson estimate: 18.7 Å2 / Rsym value: 0.086 |
Reflection shell | Resolution: 2.3→2.38 Å / Num. unique all: 3452 / Rsym value: 0.363 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Experimental electron density map from Hg SIRAS density modified phases Resolution: 2.3→19.96 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 248233.08 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.848 Å2 / ksol: 0.368286 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→19.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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