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Yorodumi- PDB-1gg1: CRYSTAL STRUCTURE ANALYSIS OF DAHP SYNTHASE IN COMPLEX WITH MN2+ ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gg1 | ||||||
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Title | CRYSTAL STRUCTURE ANALYSIS OF DAHP SYNTHASE IN COMPLEX WITH MN2+ AND 2-PHOSPHOGLYCOLATE | ||||||
Components | 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Wagner, T. / Shumilin, I.A. / Bauerle, R. / Kretsinger, R.H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Structure of 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase from Escherichia coli: comparison of the Mn(2+)*2-phosphoglycolate and the Pb(2+)*2-phosphoenolpyruvate complexes and implications for catalysis. Authors: Wagner, T. / Shumilin, I.A. / Bauerle, R. / Kretsinger, R.H. #1: Journal: Structure / 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. #2: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gg1.cif.gz | 276.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gg1.ent.gz | 222 KB | Display | PDB format |
PDBx/mmJSON format | 1gg1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gg/1gg1 ftp://data.pdbj.org/pub/pdb/validation_reports/gg/1gg1 | HTTPS FTP |
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-Related structure data
Related structure data | |
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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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Details | The biological assembly is a homotetramer constructed from chains A,B,C, and D. |
-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-PGA / #3: Chemical | ChemComp-MN / #4: Chemical | ChemComp-SO4 / #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: 2.5 Å3/Da / Density % sol: 50.09 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.7 Details: PEG 1000, 1,3-bis[tris(hydroxy-methyl)methylamino]propane, manganese sulfate, lithium sulfate, 2-phosphoglycolic acid, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97935 |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Oct 10, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97935 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 98421 / Num. obs: 98421 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 19.2 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 6.7 / Num. unique all: 9630 / % possible all: 96.3 |
Reflection | *PLUS Num. measured all: 357597 |
Reflection shell | *PLUS % possible obs: 96.3 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||
Refine LS restraints | *PLUS
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