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Yorodumi- PDB-5yg9: Crystal structure of ribose-1,5-bisphosphate isomerase mutant C13... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yg9 | ||||||
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Title | Crystal structure of ribose-1,5-bisphosphate isomerase mutant C135S from Pyrococcus horikoshii OT3 in complex with ribose-1,5-bisphosphate, AMP and GMP | ||||||
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 / pentose catabolic process / cellular biosynthetic process Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 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 | 5yg9.cif.gz | 207.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yg9.ent.gz | 164.9 KB | Display | PDB format |
PDBx/mmJSON format | 5yg9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yg/5yg9 ftp://data.pdbj.org/pub/pdb/validation_reports/yg/5yg9 | HTTPS FTP |
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-Related structure data
Related structure data | 5yfjSC 5yfsC 5yftC 5yfuC 5yfvC 5yfwC 5yfxC 5yg5C 5yg6C 5yg7C 5yg8C 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
-Protein / Sugars , 2 types, 6 molecules ABC
#1: Protein | Mass: 36440.289 Da / Num. of mol.: 3 / Mutation: C135S 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 #2: Sugar | |
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-Non-polymers , 5 types, 219 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-MPD / ( | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.31 Å3/Da / Density % sol: 62.85 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.7 M NaCl, 3% PEG 6000, 30% 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: Mar 10, 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: 2.8→85.6 Å / Num. obs: 35799 / % possible obs: 100 % / Redundancy: 11.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.045 / Rrim(I) all: 0.154 / Net I/σ(I): 15.6 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 100
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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: 2.8→85.6 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.897 / SU B: 11.309 / SU ML: 0.221 / SU R Cruickshank DPI: 0.915 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.915 / ESU R Free: 0.314 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: 148.79 Å2 / Biso mean: 37.725 Å2 / Biso min: 6.69 Å2
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Refinement step | Cycle: final / Resolution: 2.8→85.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.873 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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