+Open data
-Basic information
Entry | Database: PDB / ID: 1umg | |||||||||
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Title | Crystal structure of fructose-1,6-bisphosphatase | |||||||||
Components | 385aa long conserved hypothetical protein | |||||||||
Keywords | HYDROLASE / fructose-1 / 6-bisphosphatase / Hyperthermophilic archaea / alpha-beta-beta-alpha four layer sandwich / magnesium ion / phosphatase / octamer / three metal-assisted mechanism | |||||||||
Function / homology | Function and homology information NADPH regeneration / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / dephosphorylation / gluconeogenesis / magnesium ion binding Similarity search - Function | |||||||||
Biological species | Sulfolobus tokodaii str. 7 (archaea) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å | |||||||||
Authors | Nishimasu, H. / Fushinobu, S. / Shoun, H. / Wakagi, T. | |||||||||
Citation | Journal: Structure / Year: 2004 Title: The first crystal structure of the novel class of fructose-1,6-bisphosphatase present in thermophilic archaea. Authors: Nishimasu, H. / Fushinobu, S. / Shoun, H. / Wakagi, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1umg.cif.gz | 92.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1umg.ent.gz | 69.1 KB | Display | PDB format |
PDBx/mmJSON format | 1umg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1umg_validation.pdf.gz | 773.6 KB | Display | wwPDB validaton report |
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Full document | 1umg_full_validation.pdf.gz | 776.9 KB | Display | |
Data in XML | 1umg_validation.xml.gz | 18.3 KB | Display | |
Data in CIF | 1umg_validation.cif.gz | 27 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/um/1umg ftp://data.pdbj.org/pub/pdb/validation_reports/um/1umg | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a octamer generated from the monomer in the asymmetric unit by the operations: 1-x, 1-y, z and y, 1-x, z and 1-y, x, z and x, 1-y, -z and 1-y, 1-x, -z and 1-x, y, -z, and y, x, -z |
-Components
#1: Protein | Mass: 40098.062 Da / Num. of mol.: 1 / Fragment: residues 3-364 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus tokodaii str. 7 (archaea) / Species: Sulfolobus tokodaii / Strain: strain 7 / Gene: ST0318 / Plasmid: pET17b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) References: UniProt: Q975V5, UniProt: F9VMT6*PLUS, fructose-bisphosphatase | ||||||
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#2: Chemical | ChemComp-MG / #3: Sugar | ChemComp-2FP / | #4: Chemical | ChemComp-MPD / ( | #5: 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: 2.76 Å3/Da / Density % sol: 55.05 % |
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Crystal grow | Temperature: 298 K / Method: microbatch / pH: 8.2 Details: PEG 8000, magnesium chloride, sodium chloride, Tris-HCl, fructose-1,6-bisphosphate, pH 8.2, MICROBATCH, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 0.9712, 0.9792, 0.9794 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 2, 2003 | ||||||||||||
Radiation | Monochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.8→20 Å / Num. all: 44654 / Num. obs: 44654 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.22 % / Biso Wilson estimate: 12.9 Å2 / Rsym value: 0.04 / Net I/σ(I): 27.7 | ||||||||||||
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 8.9 / Num. unique all: 4409 / Rsym value: 0.141 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.8→19.23 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3466048.46 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 64.1639 Å2 / ksol: 0.374486 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→19.23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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