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Yorodumi- PDB-1k0g: THE CRYSTAL STRUCTURE OF AMINODEOXYCHORISMATE SYNTHASE FROM PHOSP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1k0g | ||||||
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Title | THE CRYSTAL STRUCTURE OF AMINODEOXYCHORISMATE SYNTHASE FROM PHOSPHATE 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 / MOLECULAR REPLACEMENT / Resolution: 2.05 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 | 1k0g.cif.gz | 194.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k0g.ent.gz | 149.7 KB | Display | PDB format |
PDBx/mmJSON format | 1k0g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k0/1k0g ftp://data.pdbj.org/pub/pdb/validation_reports/k0/1k0g | HTTPS FTP |
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-Related structure data
Related structure data | 1k0eSC 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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2 |
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3 |
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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) / Gene: pabB / Plasmid: pKPabB / Production host: Escherichia coli (E. coli) References: UniProt: P05041, Lyases; Carbon-carbon lyases; Oxo-acid-lyases #2: Chemical | #3: Chemical | #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: 3.43 Å3/Da / Density % sol: 64.2 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES pH7.5, 1.6M Na/K Phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 298K (PROTEIN SOLUTION: 50mM MOPS pH 7 50mM KCL, 5mM MG CL2, 2 mM DTT, 40.2 MG/ML PROTEIN. WELL SOL 0.1 M NA ...Details: 0.1M HEPES pH7.5, 1.6M Na/K Phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 298K (PROTEIN SOLUTION: 50mM MOPS pH 7 50mM KCL, 5mM MG CL2, 2 mM DTT, 40.2 MG/ML PROTEIN. WELL SOL 0.1 M NA HEPES pH 7.5, 0.8 M NA PHOSPHATE, 0.8 M K PHOSPHATE) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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-ID / Wavelength: 1.0597 / Wavelength: 1.06 Å | |||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 17, 2000 | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.05→20 Å / Num. all: 348268 / Num. obs: 88221 / % possible obs: 99.6 % / Redundancy: 4 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 28.1 | |||||||||
Reflection shell | Resolution: 2.05→2.16 Å / Redundancy: 4 % / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 2.7 / % possible all: 98.6 | |||||||||
Reflection | *PLUS Num. measured all: 348268 | |||||||||
Reflection shell | *PLUS % possible obs: 98.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PABB GROWN IN FORMATE, PDB ENTRY 1K0E Resolution: 2.05→10 Å / Num. parameters: 28923 / Num. restraintsaints: 27487 / 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: METHOD USED : MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-22 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 7227 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→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: 5.3 % / Rfactor Rwork: 0.173 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: s_plane_restr / Dev ideal: 0.023 |