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Open data
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Basic information
Entry | Database: PDB / ID: 1b9b | ||||||
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Title | TRIOSEPHOSPHATE ISOMERASE OF THERMOTOGA MARITIMA | ||||||
![]() | PROTEIN (TRIOSEPHOSPHATE ISOMERASE) | ||||||
![]() | ISOMERASE / THERMOPHILIC / THERMOTOGA MARITIMA | ||||||
Function / homology | ![]() phosphoglycerate kinase / phosphoglycerate kinase activity / triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / ADP binding / fatty acid biosynthetic process / phosphorylation / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Maes, D. / Wierenga, R.K. | ||||||
![]() | ![]() Title: The crystal structure of triosephosphate isomerase (TIM) from Thermotoga maritima: a comparative thermostability structural analysis of ten different TIM structures. Authors: Maes, D. / Zeelen, J.P. / Thanki, N. / Beaucamp, N. / Alvarez, M. / Thi, M.H. / Backmann, J. / Martial, J.A. / Wyns, L. / Jaenicke, R. / Wierenga, R.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 111 KB | Display | ![]() |
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PDB format | ![]() | 86.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451.1 KB | Display | ![]() |
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Full document | ![]() | 469.7 KB | Display | |
Data in XML | ![]() | 22.5 KB | Display | |
Data in CIF | ![]() | 29.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1bimS S: Starting model for refinement |
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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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2 |
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Unit cell |
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Details | THIS TIM FROM A HYPERTHERMOPHILIC ORGANISM EXISTS IN VIVO AS A PGK-TIM FUSION PROTEIN. THE RECOMBINANT SEPARATE TIM-ENZYME IS ALSO HYPERTHERMOPHILIC. IT IS A TETRAMER. THE TETRAMER IS FORMED BY APPLYING THE CRYSTALLOGRAPHIC TWOFOLD AXIS ON THE ASYMETRIC UNIT (A DIMER). THE MAIN INTERDIMERIC CONTACTS ARE 2 DISULFIDE BONDS. |
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Components
#1: Protein | Mass: 28554.045 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: A SULFATE MOLECULE IS OBSERVED IN THE ACTIVE SITE OF BOTH SUBUNITS Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.16 Å3/Da / Density % sol: 70 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.0 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 15, 1996 / Details: DOUBLE FOCUSSING MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→20 Å / Num. all: 22000 / Num. obs: 22000 / % possible obs: 97.8 % / Redundancy: 3.1 % / Biso Wilson estimate: 38.7 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.07 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.85→2.9 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 6.7 / Rsym value: 0.247 / % possible all: 90 |
Reflection | *PLUS Num. measured all: 88489 |
Reflection shell | *PLUS % possible obs: 90 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: BACILLUS STEAROTHERMOPHILUS TIM (PDB ENTRY 1BIM) Resolution: 2.85→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: BULK SOLVENT MODEL / Bsol: 53 Å2 / ksol: 0.289 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.85→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.85→2.9 Å / Total num. of bins used: 21
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.4 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.211 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.33 / % reflection Rfree: 5 % / Rfactor Rwork: 0.36 |