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Yorodumi- PDB-2j91: Crystal structure of Human Adenylosuccinate Lyase in complex with AMP -
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-Basic information
Entry | Database: PDB / ID: 2j91 | |||||||||
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Title | Crystal structure of Human Adenylosuccinate Lyase in complex with AMP | |||||||||
Components | ADENYLOSUCCINATE LYASE | |||||||||
Keywords | LYASE / DISEASE MUTATION / ADENYLOSUCCINASE / SUCCINO AMP-LYASE / PURINE BIOSYNTHESIS / ADENYLOSUCCINATE LYASE / ADENYLOSUCCINASE DEFICIENCY / AMP / ADSL / SAICAR / PURINE / S-AMP / EPILEPSY | |||||||||
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 / response to nutrient / aerobic respiration / 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 / Resolution: 1.8 Å | |||||||||
Authors | Stenmark, P. / Moche, M. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Edwards, A. / Ericsson, U.B. / Flodin, S. / Flores, A. ...Stenmark, P. / Moche, M. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Edwards, A. / Ericsson, U.B. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Holmberg Schiavone, L. / Hogbom, M. / Johansson, I. / Karlberg, T. / Kosinska, U. / Kotenyova, T. / Magnusdottir, A. / Nilsson, M.E. / Nilsson-Ehle, P. / Nyman, T. / Ogg, D. / Persson, C. / Sagemark, J. / Sundstrom, M. / Uppenberg, J. / Uppsten, M. / Thorsell, A.G. / van Den Berg, S. / Wallden, K. / Weigelt, J. / Nordlund, P. | |||||||||
Citation | Journal: To be Published Title: Crystal Structure of Human Adenylosuccinate Lyase Authors: Stenmark, P. / Moche, M. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Edwards, A. / Ericsson, U.B. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. ...Authors: Stenmark, P. / Moche, M. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Edwards, A. / Ericsson, U.B. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Holmberg Schiavone, L. / Hogbom, M. / Johansson, I. / Karlberg, T. / Kosinska, U. / Kotenyova, T. / Magnusdottir, A. / Nilsson, M.E. / Nilsson-Ehle, P. / Nyman, T. / Ogg, D. / Persson, C. / Sagemark, J. / Sundstrom, M. / Uppenberg, J. / Uppsten, M. / Thorsell, A.G. / Van Den Berg, S. / Wallden, K. / Weigelt, J. / Nordlund, P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2j91.cif.gz | 400.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2j91.ent.gz | 325.7 KB | Display | PDB format |
PDBx/mmJSON format | 2j91.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2j91_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 2j91_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 2j91_validation.xml.gz | 82.9 KB | Display | |
Data in CIF | 2j91_validation.cif.gz | 120.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j9/2j91 ftp://data.pdbj.org/pub/pdb/validation_reports/j9/2j91 | HTTPS FTP |
-Related structure data
Related structure data | 1yisS S: Starting model for refinement |
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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: 57220.574 Da / Num. of mol.: 4 / Fragment: RESIDUES 1-481 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P30566, adenylosuccinate lyase #2: Chemical | ChemComp-AMP / #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, GLN 63 TO ARG ENGINEERED RESIDUE IN CHAIN B, GLN 63 TO ARG ...ENGINEERED | Sequence details | POSITION 63 WAS MUTATED DURING PCR TO A R. IT IS A Q63R MUTATION. | |
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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: 2.08 Å3/Da / Density % sol: 41 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.97973 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 11, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97973 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→25 Å / Num. obs: 176155 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.9 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 4.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1YIS Resolution: 1.8→106.6 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.114 / SU ML: 0.082 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.81 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→106.6 Å
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Refine LS restraints |
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