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Yorodumi- PDB-6a34: Crystal structure of 5-methylthioribose 1-phosphate isomerase fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6a34 | ||||||
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Title | Crystal structure of 5-methylthioribose 1-phosphate isomerase from Pyrococcus horikoshii OT3 - Form I | ||||||
Components | Putative methylthioribose-1-phosphate isomerase | ||||||
Keywords | ISOMERASE / Methionine salvage pathway / PH0702 / Cis-phosphoenolate intermediate / Hydride transfer | ||||||
Function / homology | Function and homology information S-methyl-5-thioribose-1-phosphate isomerase / S-methyl-5-thioribose-1-phosphate isomerase activity / L-methionine salvage from S-adenosylmethionine Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii OT3 (archaea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å | ||||||
Authors | Kanaujia, S.P. / Gogoi, P. / Mordina, P. | ||||||
Funding support | India, 1items
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Citation | Journal: J. Struct. Biol. / Year: 2019 Title: Structural insights into the catalytic mechanism of 5-methylthioribose 1-phosphate isomerase. Authors: Gogoi, P. / Mordina, 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 | 6a34.cif.gz | 156.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6a34.ent.gz | 123.2 KB | Display | PDB format |
PDBx/mmJSON format | 6a34.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a3/6a34 ftp://data.pdbj.org/pub/pdb/validation_reports/a3/6a34 | HTTPS FTP |
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-Related structure data
Related structure data | 6a35C 1t5oS 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
#1: Protein | Mass: 40432.480 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii OT3 (archaea) / Strain: OT-3 / Gene: PH0702 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) References: UniProt: O58433, S-methyl-5-thioribose-1-phosphate isomerase #2: Chemical | ChemComp-HEZ / #3: 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: 2.76 Å3/Da / Density % sol: 55.54 % |
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Crystal grow | Temperature: 277 K / Method: microbatch / pH: 5.6 Details: 0.1M sodium citrate tribasic dihydrate pH 5.6, 2.5M 1,6-hexanediol |
-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 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: 2.3→84.87 Å / Num. obs: 39641 / % possible obs: 100 % / Redundancy: 8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.024 / Rrim(I) all: 0.069 / Net I/σ(I): 18.9 / Num. measured all: 316498 / Scaling rejects: 31 | ||||||||||||||||||||||||
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: 1T5O Resolution: 2.3→55.63 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.931 / SU B: 6.257 / SU ML: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.268 / ESU R Free: 0.219 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: 133.93 Å2 / Biso mean: 47.248 Å2 / Biso min: 21.53 Å2
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Refinement step | Cycle: final / Resolution: 2.3→55.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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