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Yorodumi- PDB-1mf1: Structure of the Recombinant Mouse-Muscle Adenylosuccinate Synthe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mf1 | ||||||
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Title | Structure of the Recombinant Mouse-Muscle Adenylosuccinate Synthetase Complexed with AMP | ||||||
Components | Adenylosuccinate Synthetase | ||||||
Keywords | LIGASE / Purine biosynthesis / GTP-binding / Multigene family | ||||||
Function / homology | Function and homology information Purine ribonucleoside monophosphate biosynthesis / purine nucleotide metabolic process / adenylosuccinate synthase / adenylosuccinate synthase activity / aspartate metabolic process / IMP metabolic process / 'de novo' AMP biosynthetic process / AMP salvage / actin filament binding / GTPase activity ...Purine ribonucleoside monophosphate biosynthesis / purine nucleotide metabolic process / adenylosuccinate synthase / adenylosuccinate synthase activity / aspartate metabolic process / IMP metabolic process / 'de novo' AMP biosynthetic process / AMP salvage / actin filament binding / GTPase activity / GTP binding / magnesium ion binding / identical protein binding / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Iancu, C.V. / Borza, T. / Fromm, H.J. / Honzatko, R.B. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Feedback inhibition and product complexes of recombinant mouse muscle adenylosuccinate synthetase. Authors: Iancu, C.V. / Borza, T. / Fromm, H.J. / Honzatko, R.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mf1.cif.gz | 95.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mf1.ent.gz | 73.6 KB | Display | PDB format |
PDBx/mmJSON format | 1mf1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mf1_validation.pdf.gz | 779.8 KB | Display | wwPDB validaton report |
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Full document | 1mf1_full_validation.pdf.gz | 791.8 KB | Display | |
Data in XML | 1mf1_validation.xml.gz | 19 KB | Display | |
Data in CIF | 1mf1_validation.cif.gz | 25.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mf/1mf1 ftp://data.pdbj.org/pub/pdb/validation_reports/mf/1mf1 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological unit is a dimer. The other monomer is generated by:2-y, 2-x, 1/2-z. |
-Components
#1: Protein | Mass: 50321.301 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Adss1 / Plasmid: Pet28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P28650, adenylosuccinate synthase |
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#2: Chemical | ChemComp-ACT / |
#3: Chemical | ChemComp-AMP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.58 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU |
Detector | Type: RIGAKU / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.7→49.7 Å / Num. all: 14816 / Num. obs: 14742 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2.7→2.8 Å / % possible all: 99.9 |
Reflection | *PLUS Num. measured all: 152538 / Rmerge(I) obs: 0.062 |
Reflection shell | *PLUS % possible obs: 99.9 % / Rmerge(I) obs: 0.33 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→15 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.7→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.027
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Refinement | *PLUS Lowest resolution: 15 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.265 / Rfactor Rwork: 0.219 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.397 / Rfactor Rwork: 0.345 |