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- PDB-5yfj: Crystal structure of ribose-1,5-bisphosphate isomerase from Pyroc... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5yfj | ||||||
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Title | Crystal structure of ribose-1,5-bisphosphate isomerase from Pyrococcus horikoshii OT3 in complex with ribulose-1,5-bisphosphate | ||||||
![]() | Ribose 1,5-bisphosphate isomerase | ||||||
![]() | ISOMERASE / NMP degradation pathway / Ribose-1 / 5-bisphosphate / Rossmann-like fold | ||||||
Function / homology | ![]() ribose-1,5-bisphosphate isomerase / ribose 1,5-bisphosphate isomerase activity / S-methyl-5-thioribose-1-phosphate isomerase activity / pentose catabolic process / L-methionine salvage from methylthioadenosine Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gogoi, P. / Kanaujia, S.P. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A presumed homologue of the regulatory subunits of eIF2B functions as ribose-1,5-bisphosphate isomerase in Pyrococcus horikoshii OT3. Authors: Gogoi, P. / Kanaujia, S.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 214.8 KB | Display | ![]() |
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PDB format | ![]() | 170.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 40.5 KB | Display | |
Data in CIF | ![]() | 58.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5yfsC ![]() 5yftC ![]() 5yfuC ![]() 5yfvC ![]() 5yfwC ![]() 5yfxC ![]() 5yg5C ![]() 5yg6C ![]() 5yg7C ![]() 5yg8C ![]() 5yg9C ![]() 5ygaC ![]() 3vm6S 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
-Protein / Sugars , 2 types, 6 molecules ABC![](data/chem/img/RUB.gif)
![](data/chem/img/RUB.gif)
#1: Protein | Mass: 36456.352 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3 Gene: PH0208 / Plasmid: pET22b / Production host: ![]() ![]() References: UniProt: O57947, ribose-1,5-bisphosphate isomerase #2: Sugar | |
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-Non-polymers , 5 types, 516 molecules ![](data/chem/img/K.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-MPD / ( | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 62.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.7 M NaCl, 3% PEG 6000, 25% MPD |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | |||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 31, 2016 / Details: VariMax HF | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.2→85.69 Å / Num. obs: 72651 / % possible obs: 99.5 % / Redundancy: 9.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.031 / Rrim(I) all: 0.098 / Net I/σ(I): 17.8 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3VM6 Resolution: 2.2→85.69 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.102 / SU ML: 0.103 / SU R Cruickshank DPI: 0.1603 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.147 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 106.86 Å2 / Biso mean: 36.644 Å2 / Biso min: 16.36 Å2
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Refinement step | Cycle: final / Resolution: 2.2→85.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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