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Yorodumi- PDB-1nht: ENTRAPMENT OF 6-THIOPHOSPHORYL-IMP IN THE ACTIVE SITE OF CRYSTALL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nht | ||||||
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Title | ENTRAPMENT OF 6-THIOPHOSPHORYL-IMP IN THE ACTIVE SITE OF CRYSTALLINE ADENYLOSUCCINATE SYNTHETASE FROM ESCHERICHIA COLI DATA COLLECTED AT 100K | ||||||
Components | ADENYLOSUCCINATE SYNTHETASE | ||||||
Keywords | LIGASE / SYNTHETASE / PURINE NUCLEOTIDE BIOSYNTHESIS / GTP-HYDROLYSING ENZYMES | ||||||
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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | ||||||
Authors | Poland, B.W. / Bruns, C.A. / Fromm, H.J. / Honzatko, R.B. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1997 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: Journal: J.Mol.Biol. / Year: 1995 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: Journal: J.Biol.Chem. / Year: 1993 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nht.cif.gz | 140.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nht.ent.gz | 110.2 KB | Display | PDB format |
PDBx/mmJSON format | 1nht.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nht_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 1nht_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 1nht_validation.xml.gz | 25.9 KB | Display | |
Data in CIF | 1nht_validation.cif.gz | 38.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nh/1nht ftp://data.pdbj.org/pub/pdb/validation_reports/nh/1nht | HTTPS FTP |
-Related structure data
-Links
-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) Escherichia coli (E. coli) / Strain: PUR A STRAIN H1238 / References: UniProt: P0A7D4, adenylosuccinate synthase |
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-Non-polymers , 5 types, 458 molecules
#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: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.72 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 100 K / pH: 6.5 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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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: 22201 / % possible obs: 98 % / Observed criterion σ(I): 4 / Redundancy: 5.5 % / Rmerge(I) obs: 0.079 |
Reflection | *PLUS Highest resolution: 2.5 Å / Num. measured all: 161473 |
Reflection shell | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 2.61 Å / % possible obs: 96 % |
-Processing
Software |
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Refinement | Resolution: 2.5→5 Å Details: THERE ARE TWO REGIONS THAT ARE DISORDERED AT POSITIONS 121 - 130, 298 - 303 AND ONE RESIDUE 416 THAT DIVERGE FROM THE DNA SEQUENCE GIVEN IN PIR:A61592. RESIDUE 416 IS GLYCINE IN THE ENTRY.
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Displacement parameters | Biso mean: 17 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→5 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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