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Yorodumi- PDB-1kfl: Crystal structure of phenylalanine-regulated 3-deoxy-D-arabino-he... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kfl | ||||||
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Title | Crystal structure of phenylalanine-regulated 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (DAHP synthase) from E.coli complexed with Mn2+, PEP, and Phe | ||||||
Components | 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase | ||||||
Keywords | LYASE / beta/alpha barrel / allosteric inhibition / feedback regulation / aromatic biosynthetic pathway | ||||||
Function / homology | Function and homology information 3-deoxy-7-phosphoheptulonate synthase / 3-deoxy-7-phosphoheptulonate synthase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å | ||||||
Authors | Shumilin, I.A. / Zhao, C. / Bauerle, R. / Kretsinger, R.H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Allosteric inhibition of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase alters the coordination of both substrates. Authors: Shumilin, I.A. / Zhao, C. / Bauerle, R. / Kretsinger, R.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kfl.cif.gz | 536.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kfl.ent.gz | 445.2 KB | Display | PDB format |
PDBx/mmJSON format | 1kfl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kfl_validation.pdf.gz | 560.2 KB | Display | wwPDB validaton report |
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Full document | 1kfl_full_validation.pdf.gz | 643.1 KB | Display | |
Data in XML | 1kfl_validation.xml.gz | 105.2 KB | Display | |
Data in CIF | 1kfl_validation.cif.gz | 132.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kf/1kfl ftp://data.pdbj.org/pub/pdb/validation_reports/kf/1kfl | HTTPS FTP |
-Related structure data
Related structure data | 1qr7S 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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Details | The biological assembly is a tetramer, two tetramers, ABCD and EFGH, reside in the asymmetric unit. |
-Components
#1: Protein | Mass: 38434.660 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: aroG / Plasmid: pTTG6 / Production host: Escherichia coli (E. coli) / Strain (production host): CB650 References: UniProt: P00886, UniProt: P0AB91*PLUS, EC: 4.1.2.15 #2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-PHE / #5: Chemical | ChemComp-PEP / |
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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: 2.84 Å3/Da / Density % sol: 56.75 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.1 Details: PEG 4000, lithium sulfate, manganese sulfate, phosphoenolpyruvate, phenylalanine, bis-tris-propane, pH 8.1, VAPOR DIFFUSION, HANGING DROP at 295K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 58 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97165 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 15, 2000 / Details: mirrors |
Radiation | Monochromator: Sagitally focused Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97165 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. all: 84564 / Num. obs: 84546 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 38.6 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 24 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 5.3 / % possible all: 98.7 |
Reflection | *PLUS Highest resolution: 2.8 Å / Num. obs: 84564 / % possible obs: 99.4 % / Rmerge(I) obs: 0.076 |
Reflection shell | *PLUS % possible obs: 98.7 % / Rmerge(I) obs: 0.313 |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: PDB ENTRY 1QR7 Resolution: 2.8→20 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
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Refinement | *PLUS % reflection Rfree: 3 % / Rfactor all: 0.219 / Rfactor Rfree: 0.246 / Rfactor Rwork: 0.218 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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