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- PDB-2h6r: Crystal Structure of triosephosphate isomerase (TIM) from Methano... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2h6r | ||||||
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Title | Crystal Structure of triosephosphate isomerase (TIM) from Methanocaldococcus jannaschii | ||||||
![]() | Triosephosphate isomerase | ||||||
![]() | ISOMERASE / beta-alpha barrel | ||||||
Function / homology | ![]() triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / gluconeogenesis / glycolytic process / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gayathri, P. / Banerjee, M. / Vijayalakshmi, A. / Balaram, H. / Balaram, P. / Murthy, M.R.N. | ||||||
![]() | ![]() Title: Structure of triosephosphate isomerase (TIM) from Methanocaldococcus jannaschii Authors: Gayathri, P. / Banerjee, M. / Vijayalakshmi, A. / Azeez, S. / Balaram, H. / Balaram, P. / Murthy, M.R.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 305.6 KB | Display | ![]() |
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PDB format | ![]() | 248.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 507.5 KB | Display | ![]() |
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Full document | ![]() | 578.3 KB | Display | |
Data in XML | ![]() | 67.4 KB | Display | |
Data in CIF | ![]() | 89.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1hg3S 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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Components
#1: Protein | Mass: 23271.996 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: DSM 2661 / Gene: TPIA / Plasmid: pTrc99A / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.44 % |
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Crystal grow | Temperature: 291 K / Method: microbatch / pH: 8 Details: 30% PEG 3350, 0.2M Magnesium chloride, 0.1M Tris pH 8.0, microbatch, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: MAC Science DIP-2040 / Detector: IMAGE PLATE / Date: Mar 20, 2006 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.3→50 Å / Num. all: 76266 / Num. obs: 76266 / % possible obs: 96.3 % / Redundancy: 14.26 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 20.15 | ||||||||||||||||||||||||||||||
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 6.3 / Num. unique all: 7537 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1HG3 Resolution: 2.3→34.28 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 80028.33 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: The structure was refined using modified CNS files for tetartohedral twinning (Barends, et al., 2005, Acta Cryst D61, 613-621). The crystal structure has been determined from a ...Details: The structure was refined using modified CNS files for tetartohedral twinning (Barends, et al., 2005, Acta Cryst D61, 613-621). The crystal structure has been determined from a tetartohedrally twinned crystal. The twinning operator are (h,k,l)(k,h,-l)(-k,-h,-l)(-h,-k,l) and the twinning fraction are 0.25, 0.25, 0.25, 0.25.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.1616 Å2 / ksol: 0.364509 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→34.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.4 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 8
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Xplor file |
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