[English] 日本語
Yorodumi- PDB-5yga: Crystal structure of ribose-1,5-bisphosphate isomerase mutant D20... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yga | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
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 | |||||||||
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: 2.45 Å | |||||||||
Authors | Gogoi, P. / Kanaujia, S.P. | |||||||||
Funding support | India, 1items
| |||||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5yga.cif.gz | 210.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5yga.ent.gz | 167.7 KB | Display | PDB format |
PDBx/mmJSON format | 5yga.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yg/5yga ftp://data.pdbj.org/pub/pdb/validation_reports/yg/5yga | 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 (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein / Sugars , 2 types, 6 molecules ABC
#1: Protein | Mass: 36455.367 Da / Num. of mol.: 3 / 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 #2: Sugar | |
---|
-Non-polymers , 5 types, 310 molecules
#3: Chemical | ChemComp-MPD / ( | ||||||
---|---|---|---|---|---|---|---|
#4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.31 Å3/Da / Density % sol: 62.84 % |
---|---|
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 | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å | ||||||||||||||||||||||||
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
|
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR | Model details: Phaser MODE: MR_AUTO
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.45→85.56 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.45→2.514 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|