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Yorodumi- PDB-1mto: Crystal structure of a Phosphofructokinase mutant from Bacillus s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mto | ||||||
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Title | Crystal structure of a Phosphofructokinase mutant from Bacillus stearothermophilus bound with fructose-6-phosphate | ||||||
Components | 6-phosphofructokinase | ||||||
Keywords | TRANSFERASE / phosphofructokinase / fructose-6-phosphate / tryptophan-shift | ||||||
Function / homology | Function and homology information 6-phosphofructokinase complex / 6-phosphofructokinase / 6-phosphofructokinase activity / fructose-6-phosphate binding / fructose 6-phosphate metabolic process / canonical glycolysis / monosaccharide binding / fructose 1,6-bisphosphate metabolic process / AMP binding / ATP binding ...6-phosphofructokinase complex / 6-phosphofructokinase / 6-phosphofructokinase activity / fructose-6-phosphate binding / fructose 6-phosphate metabolic process / canonical glycolysis / monosaccharide binding / fructose 1,6-bisphosphate metabolic process / AMP binding / ATP binding / identical protein binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Riley-Lovingshimer, M.R. / Ronning, D.R. / Sacchettini, J.C. / Reinhart, G.D. | ||||||
Citation | Journal: Biochemistry / Year: 2002 Title: Reversible Ligand-Induced Dissociation of a Tryptophan-Shift Mutant of Phosphofructokinase from Bacillus stearothermophilus Authors: Riley-Lovingshimer, M.R. / Ronning, D.R. / Sacchettini, J.C. / Reinhart, G.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mto.cif.gz | 466.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mto.ent.gz | 388.3 KB | Display | PDB format |
PDBx/mmJSON format | 1mto.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mto_validation.pdf.gz | 689.7 KB | Display | wwPDB validaton report |
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Full document | 1mto_full_validation.pdf.gz | 805 KB | Display | |
Data in XML | 1mto_validation.xml.gz | 65 KB | Display | |
Data in CIF | 1mto_validation.cif.gz | 92.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mt/1mto ftp://data.pdbj.org/pub/pdb/validation_reports/mt/1mto | HTTPS FTP |
-Related structure data
Related structure data | 3pfkS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 34167.852 Da / Num. of mol.: 8 / Mutation: W179Y,Y164W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Gene: pfk / Production host: Escherichia coli (E. coli) / Strain (production host): DF1020 / References: UniProt: P00512, 6-phosphofructokinase #2: Sugar | ChemComp-F6P / |
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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: 2.368 Å3/Da / Density % sol: 44.5707 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 8000, Sodium Cacodylate, Calcium Acetate, Fructose-6-phosphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Mar 5, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→29.84 Å / Num. obs: 46829 / Observed criterion σ(F): 0 |
Reflection | *PLUS Highest resolution: 3.1 Å / % possible obs: 91.6 % / Num. measured all: 106908 / Rmerge(I) obs: 0.101 |
Reflection shell | *PLUS % possible obs: 89.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3PFK Resolution: 3.2→29.84 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 190041.81 / Data cutoff high rms absF: 190041.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.250378 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.2→29.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.4 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 3.1 Å / Num. reflection obs: 32894 / Rfactor Rfree: 0.2746 / Rfactor Rwork: 0.1787 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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