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Yorodumi- PDB-3drw: Crystal Structure of a Phosphofructokinase from Pyrococcus horiko... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3drw | ||||||
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Title | Crystal Structure of a Phosphofructokinase from Pyrococcus horikoshii OT3 with AMP | ||||||
Components | ADP-specific phosphofructokinase | ||||||
Keywords | TRANSFERASE / 6-phosphofructokinase / Pyrococcus horikoshii / AMP / ADP / Glycolysis / Kinase / Magnesium / Metal-binding / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information ADP-specific phosphofructokinase / ADP-specific phosphofructokinase activity / phosphofructokinase activity / ADP-specific glucokinase activity / fructose metabolic process / glycolytic process / glucose metabolic process / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Singer, A.U. / Skarina, T. / Kochinyan, S. / Brown, G. / Cuff, M.E. / Edwards, A.M. / Joachimiak, A. / Savchenko, A. / Yakunin, A.F. / Jia, Z. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: ADP-dependent 6-phosphofructokinase from Pyrococcus horikoshii OT3: structure determination and biochemical characterization of PH1645. Authors: Currie, M.A. / Merino, F. / Skarina, T. / Wong, A.H. / Singer, A. / Brown, G. / Savchenko, A. / Caniuguir, A. / Guixe, V. / Yakunin, A.F. / Jia, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3drw.cif.gz | 209.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3drw.ent.gz | 163.9 KB | Display | PDB format |
PDBx/mmJSON format | 3drw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3drw_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3drw_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3drw_validation.xml.gz | 40 KB | Display | |
Data in CIF | 3drw_validation.cif.gz | 58.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dr/3drw ftp://data.pdbj.org/pub/pdb/validation_reports/dr/3drw | HTTPS FTP |
-Related structure data
Related structure data | 1u2xSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 54495.328 Da / Num. of mol.: 2 / Fragment: phosphofructokinase / Mutation: D17A Source method: isolated from a genetically manipulated source Details: no cleavage of N-terminal 6-His tag / Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: pfkC, PH1645 / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: O59355, ADP-specific phosphofructokinase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.24 Å3/Da / Density % sol: 45.05 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 20% PEG 3350, 0.2 M Lithium Citrate plus 5 mM ADP Cryoprotected in N-paratone oil., VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 24, 2007 / Details: mirrors |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 75838 / Num. obs: 74815 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 3.2 / Num. unique all: 6856 / % possible all: 90.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1U2X molecule A Resolution: 1.9→41.45 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.497 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.151 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.37 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→41.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.944 Å / Total num. of bins used: 20
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