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Yorodumi- PDB-1hon: STRUCTURE OF GUANINE NUCLEOTIDE (GPPCP) COMPLEX OF ADENYLOSUCCINA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hon | ||||||
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Title | STRUCTURE OF GUANINE NUCLEOTIDE (GPPCP) COMPLEX OF ADENYLOSUCCINATE SYNTHETASE FROM ESCHERICHIA COLI AT PH 6.5 AND 25 DEGREE CELSIUS | ||||||
Components | ADENYLOSUCCINATE SYNTHETASEAdenylosuccinate synthase | ||||||
Keywords | LIGASE (SYNTHETASE) / PURINE NUCLEOTIDE BIOSYNTHESIS / LIGASE / GTP-BINDING ENZYMES / SYNTHETASE | ||||||
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 (E. coli) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.3 Å | ||||||
Authors | Poland, B.W. / Hou, Z. / Bruns, C. / Fromm, H.J. / Honzatko, R.B. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1996 Title: Refined crystal structures of guanine nucleotide complexes of adenylosuccinate synthetase from Escherichia coli. Authors: Poland, B.W. / Hou, Z. / 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 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 | 1hon.cif.gz | 229.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hon.ent.gz | 185.5 KB | Display | PDB format |
PDBx/mmJSON format | 1hon.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ho/1hon ftp://data.pdbj.org/pub/pdb/validation_reports/ho/1hon | 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.98982, 0.01192, -0.14184), Vector: |
-Components
#1: Protein | Mass: 47269.598 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: NATIVE P212121 CRYSTALS WERE SOAKED WITH GPPNP+MG(+2) Source: (gene. exp.) Escherichia coli (E. coli) / Strain: H1238 / References: UniProt: P0A7D4, adenylosuccinate synthase #2: Chemical | ChemComp-GNH / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42.03 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 Details: NATIVE P212121 CRYSTALS WERE SOAKED WITH GPPNP+MG(+2), pH 6.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS 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 | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 |
Detector | Type: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.3 Å / Num. obs: 36689 / % possible obs: 94 % / Redundancy: 4 % / Rmerge(I) obs: 0.089 |
Reflection shell | Highest resolution: 2.3 Å / % possible all: 84 |
Reflection | *PLUS Highest resolution: 2.3 Å / Num. measured all: 106944 |
Reflection shell | *PLUS % possible obs: 84 % |
-Processing
Software |
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Refinement | Resolution: 2.3→15 Å / σ(F): 4 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 PDB FILE.
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Displacement parameters | Biso mean: 21.38 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→15 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor all: 0.186 / Rfactor obs: 0.182 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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