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Yorodumi- PDB-6agl: Molecular basis for feedback inhibition of tyrosine-regulated 3-d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6agl | ||||||
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Title | Molecular basis for feedback inhibition of tyrosine-regulated 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase from Escherichia coli | ||||||
Components | Phospho-2-dehydro-3-deoxyheptonate aldolase, Tyr-sensitive | ||||||
Keywords | BIOSYNTHETIC PROTEIN / 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase (DAHP synthase) / Escherichia coli / aromatic amino acid biosynthesis / feedback inhibition / allosteric regulation. | ||||||
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 Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Cui, D. / Qi, J. / Wen, T. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6agl.cif.gz | 253.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6agl.ent.gz | 205.8 KB | Display | PDB format |
PDBx/mmJSON format | 6agl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6agl_validation.pdf.gz | 443.1 KB | Display | wwPDB validaton report |
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Full document | 6agl_full_validation.pdf.gz | 457.2 KB | Display | |
Data in XML | 6agl_validation.xml.gz | 24.3 KB | Display | |
Data in CIF | 6agl_validation.cif.gz | 32.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/6agl ftp://data.pdbj.org/pub/pdb/validation_reports/ag/6agl | HTTPS FTP |
-Related structure data
Related structure data | 6agmC 1kflS S: Starting model for refinement C: citing same article (ref.) |
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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: 38845.898 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: aroF, b2601, JW2582 / Production host: Escherichia coli (E. coli) References: UniProt: P00888, 3-deoxy-7-phosphoheptulonate synthase #2: 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: 2.17 Å3/Da / Density % sol: 43.4 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 24% PEG3350 and 0.2 M KF, number 23 of PEG/Ion |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 14, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 22959 / % possible obs: 97.8 % / Redundancy: 5.1 % / CC1/2: 0.996 / Rpim(I) all: 0.049 / Rsym value: 0.099 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.5→2.59 Å / Num. unique obs: 1885 / CC1/2: 0.792 / Rpim(I) all: 0.358 / Rsym value: 0.638 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KFL Resolution: 2.5→37.921 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.26
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→37.921 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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