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Yorodumi- PDB-1k0e: THE CRYSTAL STRUCTURE OF AMINODEOXYCHORISMATE SYNTHASE FROM FORMA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1k0e | ||||||
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Title | THE CRYSTAL STRUCTURE OF AMINODEOXYCHORISMATE SYNTHASE FROM FORMATE GROWN CRYSTALS | ||||||
Components | p-aminobenzoate synthase component I | ||||||
Keywords | LYASE / AMINODEOXYCHORISMATE SYNTHASE / CHORISMATE / GLUTAMINE / TRYPTOPHAN / PABA SYNTHASE / P-AMINOBENZOATE SYNTHASE | ||||||
Function / homology | Function and homology information aminodeoxychorismate synthase complex / para-aminobenzoic acid biosynthetic process / aminodeoxychorismate synthase / tryptophan binding / 4-amino-4-deoxychorismate synthase activity / folic acid biosynthetic process / tryptophan biosynthetic process / tetrahydrofolate biosynthetic process / protein heterodimerization activity / magnesium ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å | ||||||
Authors | Parsons, J.F. / Jensen, P.Y. / Pachikara, A.S. / Howard, A.J. / Eisenstein, E. / Ladner, J.E. | ||||||
Citation | Journal: Biochemistry / Year: 2002 Title: Structure of Escherichia coli aminodeoxychorismate synthase: architectural conservation and diversity in chorismate-utilizing enzymes. Authors: Parsons, J.F. / Jensen, P.Y. / Pachikara, A.S. / Howard, A.J. / Eisenstein, E. / Ladner, J.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k0e.cif.gz | 190.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k0e.ent.gz | 146.7 KB | Display | PDB format |
PDBx/mmJSON format | 1k0e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k0/1k0e ftp://data.pdbj.org/pub/pdb/validation_reports/k0/1k0e | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 51022.316 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pKPabB / Production host: Escherichia coli (E. coli) References: UniProt: P05041, Lyases; Carbon-carbon lyases; Oxo-acid-lyases #2: Chemical | #3: Chemical | ChemComp-FMT / | #4: 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: 2.1 Å3/Da / Density % sol: 41.4 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.1M sodium acetate buffer, 2.0M sodium formate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K (PROTEIN SOLUTION: 50mM MOPS pH 7.5, 50mM KCL, 5mM MG CL2, 2 mM DTT, 40.2 MG/ML ...Details: 0.1M sodium acetate buffer, 2.0M sodium formate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K (PROTEIN SOLUTION: 50mM MOPS pH 7.5, 50mM KCL, 5mM MG CL2, 2 mM DTT, 40.2 MG/ML PROTEIN. WELL SOLUTION: 0.1 M NA ACETATE pH 4.6, 2.0 M NA FORMATE) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS pH: 7.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 115 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1 / Wavelength: 1 Å | |||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 17, 2000 | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2→20 Å / Num. all: 269253 / Num. obs: 55584 / % possible obs: 91.2 % / Redundancy: 5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.5 | |||||||||
Reflection shell | Resolution: 2→2.08 Å / Redundancy: 3 % / Rmerge(I) obs: 0.208 / Mean I/σ(I) obs: 4.8 / % possible all: 90.4 | |||||||||
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 20 Å / Redundancy: 5 % / Num. measured all: 269253 / Rmerge(I) obs: 0.1 | |||||||||
Reflection shell | *PLUS % possible obs: 90.4 % / Redundancy: 3 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2→10 Å / Num. parameters: 28479 / Num. restraintsaints: 28146 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 7116 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→10 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 10 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor Rwork: 0.205 / Rfactor Rfree: 0.315 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: s_plane_restr / Dev ideal: 0.018 |