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Yorodumi- PDB-1dof: THE CRYSTAL STRUCTURE OF ADENYLOSUCCINATE LYASE FROM PYROBACULUM ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dof | ||||||
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Title | THE CRYSTAL STRUCTURE OF ADENYLOSUCCINATE LYASE FROM PYROBACULUM AEROPHILUM: INSIGHTS INTO THERMAL STABILITY AND HUMAN PATHOLOGY | ||||||
Components | ADENYLOSUCCINATE LYASE | ||||||
Keywords | LYASE / purine biosynthesis | ||||||
Function / homology | Function and homology information adenylosuccinate lyase / N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity / (S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido) succinate lyase (fumarate-forming) activity / 'de novo' AMP biosynthetic process / 'de novo' IMP biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | Pyrobaculum aerophilum (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å | ||||||
Authors | Toth, E.A. / Yeates, T.O. / Goedken, E. / Dixon, J.E. / Marqusee, S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: The crystal structure of adenylosuccinate lyase from Pyrobaculum aerophilum reveals an intracellular protein with three disulfide bonds. Authors: Toth, E.A. / Worby, C. / Dixon, J.E. / Goedken, E.R. / Marqusee, S. / Yeates, T.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dof.cif.gz | 311.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dof.ent.gz | 259.4 KB | Display | PDB format |
PDBx/mmJSON format | 1dof.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/do/1dof ftp://data.pdbj.org/pub/pdb/validation_reports/do/1dof | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 45423.250 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrobaculum aerophilum (archaea) / Plasmid: PT7-7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ZY28, adenylosuccinate lyase #2: 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: 2.35 Å3/Da / Density % sol: 47.6 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 100 mM Citric Acid, 10-20% PEG 4000, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 47.7 % | ||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ | ||||||||||||||||||||||||||||
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: X8C / Wavelength: 0.908 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 20, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.908 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→48.05 Å / Num. all: 100910 / Num. obs: 100737 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 19.01 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 24.6 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.302 / % possible all: 98.8 |
Reflection | *PLUS Rmerge(I) obs: 0.08 |
Reflection shell | *PLUS % possible obs: 98.8 % |
-Processing
Software |
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Refinement | Resolution: 2.1→50 Å / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.202 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |