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- PDB-6agm: Molecular basis for feedback inhibition of tyrosine-regulated 3-d... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6agm | ||||||
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Title | Molecular basis for feedback inhibition of tyrosine-regulated 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase from Escherichia coli | ||||||
![]() | Phospho-2-dehydro-3-deoxyheptonate aldolase, Tyr-sensitive | ||||||
![]() | BIOSYNTHETIC PROTEIN / 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase (DAHP synthase) / Escherichia coli / aromatic amino acid biosynthesis / feedback inhibition / allosteric regulation. | ||||||
Function / homology | ![]() 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 Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cui, D. / Qi, J. / Wen, T. | ||||||
![]() | ![]() Title: Molecular basis for feedback inhibition of tyrosine-regulated 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase from Escherichia coli. Authors: Cui, D. / Deng, A. / Bai, H. / Yang, Z. / Liang, Y. / Liu, Z. / Qiu, Q. / Wang, L. / Liu, S. / Zhang, Y. / Shi, Y. / Qi, J. / Wen, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 504 KB | Display | ![]() |
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PDB format | ![]() | 417.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 477.4 KB | Display | ![]() |
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Full document | ![]() | 494.4 KB | Display | |
Data in XML | ![]() | 49.9 KB | Display | |
Data in CIF | ![]() | 68.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6aglC ![]() 1qr7S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 38774.820 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: aroF, b2601, JW2582 / Production host: ![]() ![]() References: UniProt: P00888, 3-deoxy-7-phosphoheptulonate synthase #2: Chemical | ChemComp-TYR / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.74 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 16% PEG 4000, 10% 2-propanol, 0.1 M sodium citrate, pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 8, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 82353 / % possible obs: 97 % / Redundancy: 6.4 % / CC1/2: 0.997 / Rpim(I) all: 0.036 / Rsym value: 0.088 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 2→2.07 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 6902 / CC1/2: 0.651 / Rpim(I) all: 0.368 / Rsym value: 0.788 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1QR7 Resolution: 2→38.207 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.62
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→38.207 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | S33: -0 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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