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Yorodumi- PDB-1ct9: CRYSTAL STRUCTURE OF ASPARAGINE SYNTHETASE B FROM ESCHERICHIA COLI -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ct9 | ||||||
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Title | CRYSTAL STRUCTURE OF ASPARAGINE SYNTHETASE B FROM ESCHERICHIA COLI | ||||||
Components | ASPARAGINE SYNTHETASE B | ||||||
Keywords | LIGASE / AMIDOTRANSFERASE / SUBSTRATE CHANNELING / ASPARAGINE BIOSYNTHESIS | ||||||
Function / homology | Function and homology information asparagine synthase (glutamine-hydrolysing) / aspartate-ammonia ligase activity / L-asparagine biosynthetic process / asparagine synthase (glutamine-hydrolyzing) activity / asparagine biosynthetic process / amino acid catabolic process / amino acid binding / glutamine metabolic process / amino acid biosynthetic process / ATP binding ...asparagine synthase (glutamine-hydrolysing) / aspartate-ammonia ligase activity / L-asparagine biosynthetic process / asparagine synthase (glutamine-hydrolyzing) activity / asparagine biosynthetic process / amino acid catabolic process / amino acid binding / glutamine metabolic process / amino acid biosynthetic process / ATP binding / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å | ||||||
Authors | Larsen, T.M. / Boehlein, S.K. / Schuster, S.M. / Richards, N.G.J. / Thoden, J.B. / Holden, H.M. / Rayment, I. | ||||||
Citation | Journal: Biochemistry / Year: 1999 Title: Three-dimensional structure of Escherichia coli asparagine synthetase B: a short journey from substrate to product. Authors: Larsen, T.M. / Boehlein, S.K. / Schuster, S.M. / Richards, N.G. / Thoden, J.B. / Holden, H.M. / Rayment, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ct9.cif.gz | 428.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ct9.ent.gz | 344.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ct9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ct/1ct9 ftp://data.pdbj.org/pub/pdb/validation_reports/ct/1ct9 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 62575.672 Da / Num. of mol.: 4 / Mutation: C1A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) References: UniProt: ASNB_ECOLI, UniProt: P22106*PLUS, asparagine synthase (glutamine-hydrolysing) |
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-Non-polymers , 5 types, 1074 molecules
#2: Chemical | ChemComp-IUM / #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-AMP / #5: Chemical | ChemComp-GLN / #6: 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: 2.59 Å3/Da / Density % sol: 52.57 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 8000, HEPES, MAGNESIUM CHLORIDE, L-GLUTAMINE, ADENOSINE 5'-MONOPHOSPHATE, SODIUM CHLORIDE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 273K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: APS / Beamline: 19-ID / Wavelength: 0.7433 |
Detector | Type: OTHER / Detector: CCD / Date: Nov 11, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7433 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. all: 200469 / Num. obs: 200469 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.331 / % possible all: 93.6 |
Reflection | *PLUS Num. measured all: 1085969 |
Reflection shell | *PLUS % possible obs: 93.6 % |
-Processing
Software |
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Refinement | Resolution: 2→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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