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- PDB-4thi: THIAMINASE I FROM BACILLUS THIAMINOLYTICUS WITH COVALENTLY BOUND ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4thi | ||||||
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Title | THIAMINASE I FROM BACILLUS THIAMINOLYTICUS WITH COVALENTLY BOUND 4-AMINO-2,5-DIMETHYLPYRIMIDINE | ||||||
![]() | PROTEIN (THIAMINASE I) | ||||||
![]() | TRANSFERASE / THIAMIN DEGRADATION | ||||||
Function / homology | ![]() thiamine pyridinylase / thiamine pyridinylase activity / thiamine catabolic process / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Campobasso, N. / Begley, T.P. / Ealick, S.E. | ||||||
![]() | ![]() Title: Crystal structure of thiaminase-I from Bacillus thiaminolyticus at 2.0 A resolution. Authors: Campobasso, N. / Costello, C.A. / Kinsland, C. / Begley, T.P. / Ealick, S.E. #1: ![]() Title: Crystallization and Preliminary X-Ray Analysis of Thiaminase I from Bacillus Thiaminolyticus: Space Group Change Upon Freezing of Crystals Authors: Campobasso, N. / Begun, J. / Costello, C.A. / Begley, T.P. / Ealick, S.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 87.3 KB | Display | ![]() |
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PDB format | ![]() | 64.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2thiSC ![]() 3thiC 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: 40518.801 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-PYD / |
#4: Water | ChemComp-HOH / |
Nonpolymer details | SULFATE ION ON CRYSTALLOGRAPHIC TWO-FOLD SG OF CYS IS COVALENTLY BOUND TO THE C6 ATOM OF 4-AMINO- ...SULFATE ION ON CRYSTALLOG |
Sequence details | THE SWISS-PROT SEQUENCE CONTAINS A SIGNAL SEQUENCE THAT GETS PROCESSED AT THREE DIFFERENT SITES. ...THE SWISS-PROT SEQUENCE CONTAINS A SIGNAL SEQUENCE THAT GETS PROCESSED AT THREE DIFFERENT SITES. THE NUMBERING OF RESIDUES IN THIS PDB FILE IS CONSISTENT |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46 % | ||||||||||||||||||||
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Crystal grow | pH: 4.6 / Details: pH 4.60 | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PRINCETON / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9104 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 23969 / % possible obs: 89.2 % / Redundancy: 6.7 % / Rsym value: 0.046 / Net I/σ(I): 31.2 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 1.5 % / Mean I/σ(I) obs: 7.2 / Rsym value: 0.15 / % possible all: 54 |
Reflection | *PLUS Rmerge(I) obs: 0.046 |
Reflection shell | *PLUS % possible obs: 54 % / Rmerge(I) obs: 0.15 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: RM TEMP STRUCTURE 2THI Resolution: 2→30 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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