+Open data
-Basic information
Entry | Database: PDB / ID: 3o8l | ||||||
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Title | Structure of phosphofructokinase from rabbit skeletal muscle | ||||||
Components | 6-phosphofructokinase, muscle type | ||||||
Keywords | TRANSFERASE / kinase | ||||||
Function / homology | Function and homology information 6-phosphofructokinase / 6-phosphofructokinase activity / fructose 6-phosphate metabolic process / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Banaszak, K. / Chang, S.H. / Rypniewski, W. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: The Crystal Structures of Eukaryotic Phosphofructokinases from Baker's Yeast and Rabbit Skeletal Muscle. Authors: Banaszak, K. / Mechin, I. / Obmolova, G. / Oldham, M. / Chang, S.H. / Ruiz, T. / Radermacher, M. / Kopperschlager, G. / Rypniewski, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3o8l.cif.gz | 304.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3o8l.ent.gz | 243.6 KB | Display | PDB format |
PDBx/mmJSON format | 3o8l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3o8l_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 3o8l_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 3o8l_validation.xml.gz | 66.2 KB | Display | |
Data in CIF | 3o8l_validation.cif.gz | 88.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o8/3o8l ftp://data.pdbj.org/pub/pdb/validation_reports/o8/3o8l | HTTPS FTP |
-Related structure data
Related structure data | 3o8nC 3o8oSC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-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 molecule is active as a tetramer, but applying crystal symmetry does not generate a full tetramer. |
-Components
#1: Protein | Mass: 83269.102 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: PFKM / Plasmid: pET5a / Production host: Escherichia coli (E. coli) / Strain (production host): DF1020DE3 / References: UniProt: P00511, 6-phosphofructokinase #2: Chemical | ChemComp-ATP / #3: Chemical | #4: Chemical | ChemComp-PO4 / |
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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: 4.14 Å3/Da / Density % sol: 70.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.3 Details: 16% PEG 400, 0.1 M MgSO4, 0.1 M acetate buffer pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8423 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 7, 2006 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8423 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→45 Å / Num. all: 47446 / Num. obs: 47446 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.2 % / Rsym value: 0.14 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 3.2→3.26 Å / Redundancy: 11.2 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.879 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3O8O Resolution: 3.2→41 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 3.2→41 Å
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Refine LS restraints |
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Xplor file |
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