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Yorodumi- PDB-1qr7: CRYSTAL STRUCTURE OF PHENYLALANINE-REGULATED 3-DEOXY-D-ARABINO-HE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qr7 | ||||||
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Title | CRYSTAL STRUCTURE OF PHENYLALANINE-REGULATED 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE SYNTHASE FROM ESCHERICHIA COLI COMPLEXED WITH PB2+ AND PEP | ||||||
Components | PHENYLALANINE-REGULATED 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE SYNTHASE | ||||||
Keywords | LYASE / BETA-ALPHA-BARREL | ||||||
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 / Resolution: 2.6 Å | ||||||
Authors | Shumilin, I.A. / Kretsinger, R.H. / Bauerle, R.H. | ||||||
Citation | Journal: Structure Fold.Des. / Year: 1999 Title: Crystal structure of phenylalanine-regulated 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase from Escherichia coli. Authors: Shumilin, I.A. / Kretsinger, R.H. / Bauerle, R.H. #1: Journal: Proteins / Year: 1996 Title: Purification, crystallization, and preliminary crystallographic analysis of 3- deoxy-D-arabino-heptulosonate-7-phosphate synthase from Escherichia coli Authors: Shumilin, I.A. / Kretsinger, R.H. / Bauerle, R.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qr7.cif.gz | 261.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qr7.ent.gz | 211.6 KB | Display | PDB format |
PDBx/mmJSON format | 1qr7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qr7_validation.pdf.gz | 418.4 KB | Display | wwPDB validaton report |
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Full document | 1qr7_full_validation.pdf.gz | 448.7 KB | Display | |
Data in XML | 1qr7_validation.xml.gz | 30.5 KB | Display | |
Data in CIF | 1qr7_validation.cif.gz | 44.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qr/1qr7 ftp://data.pdbj.org/pub/pdb/validation_reports/qr/1qr7 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a tetramer that consists of the chains A, B, C, and D related by 222 symmetry |
-Components
#1: Protein | Mass: 38059.504 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PTA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AB91, EC: 4.1.2.15 #2: Chemical | ChemComp-PB / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-PEP / #5: 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: 2.37 Å3/Da / Density % sol: 48.01 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.8 Details: PEG 1000, ethanol, lithium sulphate, bis-tris propane pH 8.8, VAPOR DIFFUSION, HANGING DROP at 295K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8.7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 150 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.93892 |
Detector | Type: FUJI / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93892 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→18 Å / Num. all: 40409 / Num. obs: 40392 / % possible obs: 91.8 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 18.1 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.118 / Num. unique all: 2825 / % possible all: 64.6 |
Reflection shell | *PLUS % possible obs: 64.6 % / Mean I/σ(I) obs: 8.5 |
-Processing
Software |
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Refinement | Resolution: 2.6→18 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.6→18 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.6 Å / σ(F): 2 / % reflection Rfree: 9.8 % / Rfactor obs: 0.194 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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