+Open data
-Basic information
Entry | Database: PDB / ID: 7fca | ||||||
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Title | PfkB(Mycobacterium marinum) | ||||||
Components | (Fructokinase, PfkB) x 2 | ||||||
Keywords | OXIDOREDUCTASE / PfkB / kinase / sandwich | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mycobacterium marinum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å | ||||||
Authors | Li, J. / Gao, B. / Ji, R. | ||||||
Funding support | China, 1items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2021 Title: Structural analysis and functional study of phosphofructokinase B (PfkB) from Mycobacterium marinum. Authors: Gao, B. / Ji, R. / Li, Z. / Su, X. / Li, H. / Sun, Y. / Ji, C. / Gan, J. / Li, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7fca.cif.gz | 306.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7fca.ent.gz | 242.7 KB | Display | PDB format |
PDBx/mmJSON format | 7fca.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7fca_validation.pdf.gz | 504.3 KB | Display | wwPDB validaton report |
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Full document | 7fca_full_validation.pdf.gz | 526.2 KB | Display | |
Data in XML | 7fca_validation.xml.gz | 57.6 KB | Display | |
Data in CIF | 7fca_validation.cif.gz | 79.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fc/7fca ftp://data.pdbj.org/pub/pdb/validation_reports/fc/7fca | HTTPS FTP |
-Related structure data
Related structure data | 7cf8C 4u7xS 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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Unit cell |
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-Components
#1: Protein | Mass: 31707.805 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium marinum (strain ATCC BAA-535 / M) (bacteria) Strain: ATCC BAA-535 / M / Gene: pfkB, MMAR_4574 / Production host: Escherichia coli (E. coli) / References: UniProt: B2HEF4 #2: Protein | | Mass: 30231.213 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium marinum (strain ATCC BAA-535 / M) (bacteria) Strain: ATCC BAA-535 / M / Gene: pfkB, MMAR_4574 / Production host: Escherichia coli (E. coli) / References: UniProt: B2HEF4 #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-PO4 / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.79 Å3/Da / Density % sol: 55.85 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: pH 6.9, 0.49 M sodium phosphate monobasic monohydrate, 0.91 M potassium phosphate dibasic |
-Data collection
Diffraction | Mean temperature: 291 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 19, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.21→66.92 Å / Num. obs: 104442 / % possible obs: 99.8 % / Redundancy: 2 % / Biso Wilson estimate: 55.02 Å2 / CC1/2: 0.999 / Net I/σ(I): 19.84 |
Reflection shell | Resolution: 2.21→2.286 Å / Num. unique obs: 10403 / CC1/2: 0.999 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4U7X Resolution: 2.21→66.92 Å / SU ML: 0.2895 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.2678 / Stereochemistry target values: GeoStd + Monomer Library
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.07 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.21→66.92 Å
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Refine LS restraints |
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LS refinement shell |
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