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Yorodumi- PDB-1abb: CONTROL OF PHOSPHORYLASE B CONFORMATION BY A MODIFIED COFACTOR: C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1abb | ||||||
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Title | CONTROL OF PHOSPHORYLASE B CONFORMATION BY A MODIFIED COFACTOR: CRYSTALLOGRAPHIC STUDIES ON R-STATE GLYCOGEN PHOSPHORYLASE RECONSTITUTED WITH PYRIDOXAL 5'-DIPHOSPHATE | ||||||
Components | GLYCOGEN PHOSPHORYLASE B | ||||||
Keywords | GLYCOGEN PHOSPHORYLASE | ||||||
Function / homology | Function and homology information glycogen phosphorylase / glycogen phosphorylase activity / : / : / glycogen catabolic process / skeletal muscle myofibril / pyridoxal phosphate binding / nucleotide binding Similarity search - Function | ||||||
Biological species | Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.8 Å | ||||||
Authors | Leonidas, D.D. / Oikonomakos, N.G. / Papageorgiou, A.C. / Acharya, K.R. / Barford, D. / Johnson, L.N. | ||||||
Citation | Journal: Protein Sci. / Year: 1992 Title: Control of phosphorylase b conformation by a modified cofactor: crystallographic studies on R-state glycogen phosphorylase reconstituted with pyridoxal 5'-diphosphate. Authors: Leonidas, D.D. / Oikonomakos, N.G. / Papageorgiou, A.C. / Acharya, K.R. / Barford, D. / Johnson, L.N. #1: Journal: Nature / Year: 1989 Title: The Allosteric Transition of Glycogen Phosphorylase Authors: Barford, D. / Johnson, L.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1abb.cif.gz | 667.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1abb.ent.gz | 539.2 KB | Display | PDB format |
PDBx/mmJSON format | 1abb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1abb_validation.pdf.gz | 770.3 KB | Display | wwPDB validaton report |
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Full document | 1abb_full_validation.pdf.gz | 1017.9 KB | Display | |
Data in XML | 1abb_validation.xml.gz | 94.5 KB | Display | |
Data in CIF | 1abb_validation.cif.gz | 131.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ab/1abb ftp://data.pdbj.org/pub/pdb/validation_reports/ab/1abb | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: TYR 1 280 - PRO 1 281 OMEGA ANGLE = 275.327 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 2: ASP 1 320 - PRO 1 321 OMEGA ANGLE = 231.150 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 3: ALA 1 836 - PRO 1 837 OMEGA ANGLE = 329.984 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 4: TRP 2 67 - ILE 2 68 OMEGA ANGLE = 138.728 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 5: TYR 2 280 - PRO 2 281 OMEGA ANGLE = 270.308 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 6: ASP 2 320 - PRO 2 321 OMEGA ANGLE = 228.278 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 7: CIS PROLINE - PRO 2 837 8: TYR 3 280 - PRO 3 281 OMEGA ANGLE = 275.626 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 9: ASP 3 320 - PRO 3 321 OMEGA ANGLE = 249.790 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 10: ALA 3 836 - PRO 3 837 OMEGA ANGLE = 314.024 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 11: TYR 4 280 - PRO 4 281 OMEGA ANGLE = 267.181 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 12: ASP 4 320 - PRO 4 321 OMEGA ANGLE = 238.142 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 13: ALA 4 836 - PRO 4 837 OMEGA ANGLE = 317.052 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION |
-Components
#1: Protein | Mass: 95664.398 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / References: UniProt: P00489, glycogen phosphorylase #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-PDP / #4: Chemical | ChemComp-IMP / Sequence details | RESIDUE 380 WAS BUILT AS AN ISOLEUCINE AS THIS SIDE CHAIN APPEARED TO FIT THE ELECTRON DENSITY FOR ...RESIDUE 380 WAS BUILT AS AN ISOLEUCINE | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.41 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 16 ℃ / pH: 7.5 / Method: microdialysis | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.8 Å / Num. obs: 78049 / % possible obs: 98 % / Num. measured all: 107286 / Rmerge(I) obs: 0.108 |
-Processing
Software |
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Refinement | Resolution: 2.8→8 Å / σ(F): 1 /
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Refinement step | Cycle: LAST / Resolution: 2.8→8 Å
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Refine LS restraints |
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Refinement | *PLUS Num. reflection obs: 73340 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |