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Yorodumi- PDB-4xyj: Crystal structure of human phosphofructokinase-1 in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xyj | ||||||
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Title | Crystal structure of human phosphofructokinase-1 in complex with ATP and Mg, Northeast Structural Genomics Consortium Target HR9275 | ||||||
Components | ATP-dependent 6-phosphofructokinase, platelet type | ||||||
Keywords | TRANSFERASE / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information 6-phosphofructokinase complex / 6-phosphofructokinase / fructose-6-phosphate binding / 6-phosphofructokinase activity / fructose 1,6-bisphosphate metabolic process / fructose 6-phosphate metabolic process / monosaccharide binding / canonical glycolysis / Glycolysis / AMP binding ...6-phosphofructokinase complex / 6-phosphofructokinase / fructose-6-phosphate binding / 6-phosphofructokinase activity / fructose 1,6-bisphosphate metabolic process / fructose 6-phosphate metabolic process / monosaccharide binding / canonical glycolysis / Glycolysis / AMP binding / cellular response to leukemia inhibitory factor / cadherin binding / protein-containing complex binding / extracellular exosome / ATP binding / membrane / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Forouhar, F. / Webb, B.A. / Szu, F.-E. / Seetharaman, J. / Barber, D.L. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: Nature / Year: 2015 Title: Structures of human phosphofructokinase-1 and atomic basis of cancer-associated mutations. Authors: Webb, B.A. / Forouhar, F. / Szu, F.E. / Seetharaman, J. / Tong, L. / Barber, D.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xyj.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4xyj.ent.gz | 940.7 KB | Display | PDB format |
PDBx/mmJSON format | 4xyj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xy/4xyj ftp://data.pdbj.org/pub/pdb/validation_reports/xy/4xyj | HTTPS FTP |
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-Related structure data
Related structure data | 4xykC 3o8lS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
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 | TETRAMER BY GEL FILTRATION AND EM DATA |
-Components
-Protein , 1 types, 8 molecules ABCDEFGH
#1: Protein | Mass: 89144.727 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Details: platelet / Source: (gene. exp.) Homo sapiens (human) / Gene: PFKP, PFKF / Details (production host): Bac-to-Bac Expression system / Production host: unidentified baculovirus / References: UniProt: Q01813, 6-phosphofructokinase |
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-Non-polymers , 5 types, 182 molecules
#2: Chemical | ChemComp-ATP / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-PO4 / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.07 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 7 Details: 200 mM potassium thiocyanate, pH 7, and 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97907 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Sep 17, 2013 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97907 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→49.69 Å / Num. obs: 121790 / % possible obs: 93 % / Redundancy: 6.4 % / Biso Wilson estimate: 53.7 Å2 / Rsym value: 0.084 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 3.1→3.21 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.684 / Mean I/σ(I) obs: 1.84 / % possible all: 84.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3O8L Resolution: 3.1→49.69 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 451885.17 / 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: 16.4025 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.1→49.69 Å /
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.29 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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