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Yorodumi- PDB-1jeo: Crystal Structure of the Hypothetical Protein MJ1247 from Methano... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jeo | ||||||
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Title | Crystal Structure of the Hypothetical Protein MJ1247 from Methanococcus jannaschii at 2.0 A Resolution Infers a Molecular Function of 3-Hexulose-6-Phosphate isomerase. | ||||||
Components | HYPOTHETICAL PROTEIN MJ1247Hypothesis | ||||||
Keywords | ISOMERASE / RuMP pathway / phosphosugar / 3-hexulose-6-phosphate isomerase / PHI / Structural Genomics / BSGC structure funded by NIH / Protein Structure Initiative / PSI / Berkeley Structural Genomics Center | ||||||
Function / homology | Function and homology information 6-phospho-3-hexuloisomerase / hexulose-6-phosphate isomerase activity / carbohydrate derivative metabolic process / carbohydrate derivative binding / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Martinez-Cruz, L.A. / Dreyer, M.K. / Boisvert, D.C. / Yokota, H. / Martinez-Chantar, M.L. / Kim, R. / Kim, S.H. / Berkeley Structural Genomics Center (BSGC) | ||||||
Citation | Journal: Structure / Year: 2002 Title: Crystal structure of MJ1247 protein from M. jannaschii at 2.0 A resolution infers a molecular function of 3-hexulose-6-phosphate isomerase. Authors: Martinez-Cruz, L.A. / Dreyer, M.K. / Boisvert, D.C. / Yokota, H. / Martinez-Chantar, M.L. / Kim, R. / Kim, S.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jeo.cif.gz | 49.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jeo.ent.gz | 35.7 KB | Display | PDB format |
PDBx/mmJSON format | 1jeo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/je/1jeo ftp://data.pdbj.org/pub/pdb/validation_reports/je/1jeo | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | The biological assembly is a tetramer generated from the monomer in the asymmetric unit by the operations -X,-Y, Z X,-Y,-Z -X, Y,-Z |
-Components
#1: Protein | Mass: 20698.459 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Gene: mj1247 / Plasmid: SJS1244 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q58644 |
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#2: Chemical | ChemComp-CIT / |
#3: 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: 2.33 Å3/Da / Density % sol: 47.2 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 40% PEG 400, 0.1 M Tris/HCl, 0.2 M Sodium citrate, 10 mM betamercaptoethanol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 280 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Sep 15, 1999 |
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→30 Å / Num. obs: 37198 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.44 % / Biso Wilson estimate: 19.03 Å2 / Rsym value: 0.08 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 1.63 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 1.98 / Num. unique all: 982 / Rsym value: 0.32 / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. obs: 12655 / % possible obs: 94 % / Num. measured all: 37198 / Rmerge(I) obs: 0.08 |
Reflection shell | *PLUS % possible obs: 75.5 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: MJ1247 model obtained from MAD data (selenomethionine-derivatized crystals) Resolution: 2→30 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: RESIDUES 1-3 ARE DISORDERED. HENCE, THE COORDINATES OF ITS SIDE CHAIN ARE NOT INCLUDED IN THE PDB FILE.
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Displacement parameters | Biso mean: 18.4695 Å2
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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LS refinement shell |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.1891 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |