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- PDB-1jit: CRYSTAL STRUCTURE OF TETRAGONAL LYSOZYME GROWN IN PRESENCE 30% TR... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1jit | ||||||
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Title | CRYSTAL STRUCTURE OF TETRAGONAL LYSOZYME GROWN IN PRESENCE 30% TREHALOSE | ||||||
![]() | LYSOZYME![]() | ||||||
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Function / homology | ![]() Lactose synthesis / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Datta, S. / Biswal, B.K. / Vijayan, M. | ||||||
![]() | ![]() Title: The effect of stabilizing additives on the structure and hydration of proteins: a study involving tetragonal lysozyme. Authors: Datta, S. / Biswal, B.K. / Vijayan, M. #1: ![]() Title: Hydration, Mobility and Accessibility of Lysozyme: Strucutres of a Ph 6.5 Orthorhombic Form and its Low-Humidity Variant and a Comparative Study Involving 20 Crystallographically Independent Molecules Authors: Biswal, B.K. / Sukumar, N. / Vijayan, M. #2: ![]() Title: Protein Hydration and Water Structure: X-Ray Analysis of a Closely Packed Protein Crystal with Very Low Solvent Content Authors: Madhusudan, K. / Kodandapani, R. / Vijayan, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 40.8 KB | Display | ![]() |
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PDB format | ![]() | 27.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1jisC ![]() 1jiyC ![]() 1jj0C ![]() 1jj1C ![]() 1jj3C ![]() 193lS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.97 % |
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Crystal grow![]() | Temperature: 293 K / Method: liquid diffusion / pH: 4.6 Details: Na-acetate buffer, pH 4.6, 10% NaCl, 30% trehalose, LIQUID DIFFUSION at 293K |
Crystal grow | *PLUS Method: unknown |
Components of the solutions | *PLUS Conc.: 0.04 M / Common name: acetate / Details: pH4.6 |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.9→30 Å / Num. all: 10007 / Num. obs: 9275 / % possible obs: 92.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 15.1 Å2 / Rsym value: 0.064 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.9→1.97 Å / Num. unique all: 917 / Rsym value: 0.227 / % possible all: 93 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 25368 / Rmerge(I) obs: 0.064 |
Reflection shell | *PLUS % possible obs: 93 % / Num. unique obs: 917 / Rmerge(I) obs: 0.227 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 193L Resolution: 1.9→30 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 541825.36 / 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: 58.8465 Å2 / ksol: 0.417951 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 10.5 % / Rfactor obs: 0.194 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 22.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.273 / % reflection Rfree: 10.1 % / Rfactor Rwork: 0.229 |