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Yorodumi- PDB-4flc: Structural and Biochemical Characterization of Human Adenylosucci... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4flc | ||||||
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Title | Structural and Biochemical Characterization of Human Adenylosuccinate Lyase (ADSL) and the R303C ADSL Deficiency Associated Mutation | ||||||
Components | Adenylosuccinate lyase | ||||||
Keywords | LYASE / PURINE BIOSYNTHESIS / DISEASE MUTATION / PURINE METABOLISM | ||||||
Function / homology | Function and homology information AMP biosynthetic process / 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' XMP biosynthetic process / Purine ribonucleoside monophosphate biosynthesis / 'de novo' AMP biosynthetic process / AMP salvage / GMP biosynthetic process / purine nucleotide biosynthetic process ...AMP biosynthetic process / 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' XMP biosynthetic process / Purine ribonucleoside monophosphate biosynthesis / 'de novo' AMP biosynthetic process / AMP salvage / GMP biosynthetic process / purine nucleotide biosynthetic process / response to muscle activity / 'de novo' IMP biosynthetic process / response to starvation / aerobic respiration / response to nutrient / response to hypoxia / protein-containing complex / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å | ||||||
Authors | Deaton, M.K. / Ray, S.P. / Capodagli, G.C. / Calkins, L.A.F. / Sawle, L. / Ghosh, K. / Patterson, D. / Pegan, S.D. | ||||||
Citation | Journal: Biochemistry / Year: 2012 Title: Structural and Biochemical Characterization of Human Adenylosuccinate Lyase (ADSL) and the R303C ADSL Deficiency-Associated Mutation. Authors: Ray, S.P. / Deaton, M.K. / Capodagli, G.C. / Calkins, L.A. / Sawle, L. / Ghosh, K. / Patterson, D. / Pegan, S.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4flc.cif.gz | 543.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4flc.ent.gz | 432.5 KB | Display | PDB format |
PDBx/mmJSON format | 4flc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fl/4flc ftp://data.pdbj.org/pub/pdb/validation_reports/fl/4flc | HTTPS FTP |
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-Related structure data
Related structure data | 4ffxC 2j91S 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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Unit cell |
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-Components
#1: Protein | Mass: 55219.508 Da / Num. of mol.: 4 / Mutation: R303C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ADSL, AMPS / Plasmid: pET-14b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3)pLysS / References: UniProt: P30566, 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: 2.23 Å3/Da / Density % sol: 44.76 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Tris pH 8.5, 20% PEG 8000, 12.5 mM spermine tetrahydrochloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9789 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 15, 2011 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 61656 / Num. obs: 58820 / % possible obs: 95.4 % |
Reflection shell | Resolution: 2.6→2.69 Å / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 4.8 / % possible all: 97.1 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 42.54 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2J91 Resolution: 2.6→47.47 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.875 / Occupancy max: 1 / Occupancy min: 0.13 / SU B: 30.195 / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.415 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 102.23 Å2 / Biso mean: 55.108 Å2 / Biso min: 10.05 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→47.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.66 Å / Total num. of bins used: 20
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Refinement TLS params. | L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: 0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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