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Yorodumi- PDB-7ykc: crystal structure of the Phenylalanine-regulated 3-deoxy-D-arabin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ykc | ||||||
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Title | crystal structure of the Phenylalanine-regulated 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (ARO3) from Saccharomyces cerevisiae | ||||||
Components | 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase | ||||||
Keywords | BIOSYNTHETIC PROTEIN / DAHP synthase / ARO3 | ||||||
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 / mitochondrion / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||
Authors | Liu, H. / Luo, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: Commun Chem / Year: 2023 Title: Mechanistic investigation of a D to N mutation in DAHP synthase that dictates carbon flux into the shikimate pathway in yeast. Authors: Liu, H. / Xiao, Q. / Wu, X. / Ma, H. / Li, J. / Guo, X. / Liu, Z. / Zhang, Y. / Luo, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ykc.cif.gz | 306.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ykc.ent.gz | 255.5 KB | Display | PDB format |
PDBx/mmJSON format | 7ykc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ykc_validation.pdf.gz | 444 KB | Display | wwPDB validaton report |
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Full document | 7ykc_full_validation.pdf.gz | 477 KB | Display | |
Data in XML | 7ykc_validation.xml.gz | 31.6 KB | Display | |
Data in CIF | 7ykc_validation.cif.gz | 41.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yk/7ykc ftp://data.pdbj.org/pub/pdb/validation_reports/yk/7ykc | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 41129.926 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: ARO3, YDR035W, YD9673.07 / Production host: Escherichia coli B (bacteria) References: UniProt: P14843, 3-deoxy-7-phosphoheptulonate synthase |
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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: 2.26 Å3/Da / Density % sol: 45.66 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1 M Sodium chloride, 0.1 M BICINE pH 9.0, 20% v/v Polyethylene glycol monomethyl ether 550 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 3.3→105.79 Å / Num. obs: 11363 / % possible obs: 96.6 % / Redundancy: 7 % / Biso Wilson estimate: 128.97 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.047 / Rrim(I) all: 0.125 / Net I/σ(I): 9.6 / Num. measured all: 79559 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: AlphaFold2 Resolution: 3.3→34.37 Å / SU ML: 0.75 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 37.43 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.3→34.37 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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