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- PDB-1ksz: ENTRAPMENT OF 6-THIOPHOSPHORYL-IMP IN THE ACTIVE SITE OF CRYSTALL... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ksz | ||||||
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Title | ENTRAPMENT OF 6-THIOPHOSPHORYL-IMP IN THE ACTIVE SITE OF CRYSTALLINE ADENYLOSUCCINATE SYNTHETASE FROM ESCHERICHIA COLI, DATA COLLECTED AT 298K | ||||||
![]() | ADENYLOSUCCINATE SYNTHETASE | ||||||
![]() | LIGASE / SYNTHETASE / PURINE NUCLEOTIDE BIOSYNTHESIS / GTP-HYDROLYSING ENZYMES | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Poland, B.W. / Bruns, C.A. / Fromm, H.J. / Honzatko, R.B. | ||||||
![]() | ![]() Title: Entrapment of 6-thiophosphoryl-IMP in the active site of crystalline adenylosuccinate synthetase from Escherichia coli. Authors: Poland, B.W. / Bruns, C. / Fromm, H.J. / Honzatko, R.B. #1: ![]() Title: Refined Crystal Structures of Unligated Adenylosuccinate Synthetase from Escherichia Coli Authors: Silva, M.M. / Poland, B.W. / Hoffman, C.R. / Fromm, H.J. / Honzatko, R.B. #2: ![]() Title: Crystal Structure of Adenylosuccinate Synthetase from Escherichia Coli. Evidence for Convergent Evolution of GTP-Binding Domains Authors: Poland, B.W. / Silva, M.M. / Serra, M.A. / Cho, Y. / Kim, K.H. / Harris, E.M. / Honzatko, R.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 121.8 KB | Display | ![]() |
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PDB format | ![]() | 94 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 47269.598 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: A GIFT FROM DR. B. BACHMAN, GENETIC CENTER, YALE UNIVERSITY Source: (natural) ![]() ![]() |
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-Non-polymers , 5 types, 160 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/HDA.gif)
![](data/chem/img/PGS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/HDA.gif)
![](data/chem/img/PGS.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MG / |
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#3: Chemical | ChemComp-GDP / |
#4: Chemical | ChemComp-HDA / |
#5: Chemical | ChemComp-PGS / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.24 Å3/Da / Density % sol: 62.02 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 298 K / pH: 6.5 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Date: May 5, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 16429 / % possible obs: 98 % / Observed criterion σ(I): 4 / Redundancy: 5.5 % / Rmerge(I) obs: 0.097 |
Reflection | *PLUS Highest resolution: 2.8 Å / Num. measured all: 156061 |
Reflection shell | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 2.9 Å / % possible obs: 95 % |
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Processing
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Refinement | Resolution: 2.8→5 Å Details: THERE ARE TWO REGIONS THAT ARE DISORDERED AT POSITIONS 121 - 130, 298 - 303 AND ONE RESIDUE 416 THAT DIVERGES FROM THE DNA SEQUENCE GIVEN IN PIR:A61592. RESIDUE 416 IS GLYCINE IN THE PDB ENTRY.
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Displacement parameters | Biso mean: 26 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→5 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.25 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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