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- PDB-5yga: Crystal structure of ribose-1,5-bisphosphate isomerase mutant D20... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5yga | |||||||||
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Title | Crystal structure of ribose-1,5-bisphosphate isomerase mutant D204N from Pyrococcus horikoshii OT3 in complex with ribose-1,5-bisphosphate, AMP and GMP | |||||||||
![]() | 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 | ![]() | 210.3 KB | Display | ![]() |
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PDB format | ![]() | 167.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.8 MB | Display | ![]() |
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Full document | ![]() | 2.8 MB | Display | |
Data in XML | ![]() | 38.6 KB | Display | |
Data in CIF | ![]() | 54.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5yfjSC ![]() 5yfsC ![]() 5yftC ![]() 5yfuC ![]() 5yfvC ![]() 5yfwC ![]() 5yfxC ![]() 5yg5C ![]() 5yg6C ![]() 5yg7C ![]() 5yg8C ![]() 5yg9C 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
-Protein / Sugars , 2 types, 6 molecules ABC![](data/chem/img/RI2.gif)
![](data/chem/img/RI2.gif)
#1: Protein | Mass: 36455.367 Da / Num. of mol.: 3 / Mutation: D204N 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, 310 molecules ![](data/chem/img/MPD.gif)
![](data/chem/img/AMP.gif)
![](data/chem/img/K.gif)
![](data/chem/img/5GP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/AMP.gif)
![](data/chem/img/K.gif)
![](data/chem/img/5GP.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-MPD / ( | ||||||
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#4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.31 Å3/Da / Density % sol: 62.84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.7 M NaCl, 3% PEG 6000, 20% MPD, 0.1% Low Melting Agarose |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() | ||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 21, 2017 / 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: 2.45→85.56 Å / Num. obs: 53172 / % possible obs: 100 % / Redundancy: 12.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.032 / Rrim(I) all: 0.113 / Net I/σ(I): 19.6 / Num. measured all: 671257 / Scaling rejects: 232 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 100
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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: 5YFJ Resolution: 2.45→85.56 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.926 / SU B: 7.666 / SU ML: 0.171 / SU R Cruickshank DPI: 0.2808 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.281 / ESU R Free: 0.225 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: 160.36 Å2 / Biso mean: 41.908 Å2 / Biso min: 17.25 Å2
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Refinement step | Cycle: final / Resolution: 2.45→85.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.45→2.514 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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