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Yorodumi- PDB-1kkf: Complex of E. coli Adenylosuccinate Synthetase with IMP, Hadacidi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kkf | ||||||
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Title | Complex of E. coli Adenylosuccinate Synthetase with IMP, Hadacidin, Pyrophosphate, and Mg | ||||||
Components | Adenylosuccinate SynthetaseAdenylosuccinate synthase | ||||||
Keywords | LIGASE / GTP-HYDROLYSING ENZYMES / PURINE NUCLEOTIDE BIOSYNTHESIS / INDUCED FIT | ||||||
Function / homology | Function and homology information adenylosuccinate synthase / adenylosuccinate synthase activity / adenosine biosynthetic process / IMP metabolic process / 'de novo' AMP biosynthetic process / nucleobase-containing small molecule interconversion / purine nucleotide biosynthetic process / guanosine tetraphosphate binding / DNA damage response / GTP binding ...adenylosuccinate synthase / adenylosuccinate synthase activity / adenosine biosynthetic process / IMP metabolic process / 'de novo' AMP biosynthetic process / nucleobase-containing small molecule interconversion / purine nucleotide biosynthetic process / guanosine tetraphosphate binding / DNA damage response / GTP binding / magnesium ion binding / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli K12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Hou, Z. / Wang, W. / Fromm, H.J. / Honzatko, R.B. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: IMP Alone Organizes the Active Site of Adenylosuccinate Synthetase from Escherichia coli. Authors: Hou, Z. / Wang, W. / 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 | 1kkf.cif.gz | 105 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kkf.ent.gz | 78.9 KB | Display | PDB format |
PDBx/mmJSON format | 1kkf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kk/1kkf ftp://data.pdbj.org/pub/pdb/validation_reports/kk/1kkf | 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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Details | The assymmetric unit contains a single subunit. The functional system is a dimer. |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 47400.793 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Production host: Escherichia coli (E. coli) References: UniProt: P12283, UniProt: P0A7D4*PLUS, adenylosuccinate synthase |
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-Non-polymers , 5 types, 348 molecules
#2: Chemical | ChemComp-MG / |
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#3: Chemical | ChemComp-DPO / |
#4: Chemical | ChemComp-HDA / |
#5: Chemical | ChemComp-IMP / |
#6: 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: 3.1 Å3/Da / Density % sol: 60.33 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 8000, HEPES, IMP, Hadacidin, Pyrophosphate, Magnesium Acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.54178 Å |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Jan 1, 1998 / Details: Graphite monochromator |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. all: 22089 / Num. obs: 22089 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rsym value: 0.083 |
Reflection shell | Resolution: 2.55→2.75 Å / % possible all: 99 |
Reflection | *PLUS Lowest resolution: 20 Å / % possible obs: 99 % / Num. measured all: 85975 / Rmerge(I) obs: 0.083 |
Reflection shell | *PLUS % possible obs: 99 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→5 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.6→5 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 5 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.19 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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