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Yorodumi- PDB-5yfx: Crystal structure of ribose-1,5-bisphosphate isomerase mutant D20... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yfx | ||||||
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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 and AMP | ||||||
Components | Ribose 1,5-bisphosphate isomerase | ||||||
Keywords | ISOMERASE / NMP degradation pathway / Ribose-1 / 5-bisphosphate / Rossmann-like fold | ||||||
Function / homology | Function and homology information 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 | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å | ||||||
Authors | Gogoi, P. / Kanaujia, S.P. | ||||||
Funding support | India, 1items
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Citation | Journal: Sci Rep / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yfx.cif.gz | 80.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yfx.ent.gz | 58.3 KB | Display | PDB format |
PDBx/mmJSON format | 5yfx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5yfx_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 5yfx_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5yfx_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 5yfx_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yf/5yfx ftp://data.pdbj.org/pub/pdb/validation_reports/yf/5yfx | HTTPS FTP |
-Related structure data
Related structure data | 5yfjSC 5yfsC 5yftC 5yfuC 5yfvC 5yfwC 5yg5C 5yg6C 5yg7C 5yg8C 5yg9C 5ygaC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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: 36455.367 Da / Num. of mol.: 1 / Mutation: D204N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3 Gene: PH0208 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) References: UniProt: O57947, ribose-1,5-bisphosphate isomerase |
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#2: Sugar | ChemComp-RI2 / |
#3: Chemical | ChemComp-AMP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.7 M NaCl, 3% PEG 6000, 20% MPD |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 23, 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: 2.7→100.18 Å / Num. obs: 10900 / % possible obs: 100 % / Redundancy: 10.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.029 / Rrim(I) all: 0.094 / Net I/σ(I): 23 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5YFJ Resolution: 2.7→100.18 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.884 / SU B: 14.891 / SU ML: 0.289 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.366 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: 118.85 Å2 / Biso mean: 48.382 Å2 / Biso min: 12.68 Å2
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Refinement step | Cycle: final / Resolution: 2.7→100.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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