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Yorodumi- PDB-6gpb: REFINED CRYSTAL STRUCTURE OF THE PHOSPHORYLASE-HEPTULOSE 2-PHOSPH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gpb | |||||||||
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Title | REFINED CRYSTAL STRUCTURE OF THE PHOSPHORYLASE-HEPTULOSE 2-PHOSPHATE-OLIGOSACCHARIDE-AMP COMPLEX | |||||||||
Components | GLYCOGEN PHOSPHORYLASE B | |||||||||
Keywords | GLYCOGEN PHOSPHORYLASE | |||||||||
Function / homology | Function and homology information glycogen phosphorylase / glycogen phosphorylase activity / linear malto-oligosaccharide phosphorylase activity / SHG alpha-glucan 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: 2.86 Å | |||||||||
Authors | Acharya, K.R. / Johnson, L.N. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 1990 Title: Refined crystal structure of the phosphorylase-heptulose 2-phosphate-oligosaccharide-AMP complex. Authors: Johnson, L.N. / Acharya, K.R. / Jordan, M.D. / McLaughlin, P.J. #1: Journal: Glycogen Phosphorylase B: Description of the Protein Structure Title: Glycogen Phosphorylase B: Description of the Protein Structure 1 1991 Authors: Acharya, K.R. / Stuart, D.I. / Varvill, K.M. / Johnson, L.N. #2: Journal: J.Mol.Biol. / Year: 1991 Title: Structural Mechanism for Glycogen Phosphorylase Control by Phosphorylation and AMP Authors: Barford, D. / Hu, S.-H. / Johnson, L.N. #3: Journal: Biochemistry / Year: 1990 Title: Comparison of the Binding of Glucose and Glucose-1-Phosphate Derivatives to T-State Glycogen Phosphorylase B Authors: Martin, J.L. / Johnson, L.N. / Withers, S.G. #4: Journal: Nature / Year: 1989 Title: The Allosteric Transition of Glycogen Phosphorylase Authors: Barford, D. / Johnson, L.N. #5: Journal: Nature / Year: 1988 Title: Structural Changes in Glycogen Phosphorylase Induced by Phosphorylation Authors: Sprang, S.R. / Acharya, K.R. / Goldsmith, E.J. / Stuart, D.I. / Varvill, K. / Fletterick, R.J. / Madsen, N.B. / 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 | 6gpb.cif.gz | 196.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gpb.ent.gz | 153.4 KB | Display | PDB format |
PDBx/mmJSON format | 6gpb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6gpb_validation.pdf.gz | 618.2 KB | Display | wwPDB validaton report |
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Full document | 6gpb_full_validation.pdf.gz | 663.1 KB | Display | |
Data in XML | 6gpb_validation.xml.gz | 24.1 KB | Display | |
Data in CIF | 6gpb_validation.cif.gz | 38.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gp/6gpb ftp://data.pdbj.org/pub/pdb/validation_reports/gp/6gpb | 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: RESIDUE 380 IS LEU IN THE SEQUENCE (K.NAKANO,P.K.HWANG, R.J.FLETTERICK, FEBS LETT., V. 204, P. 283, 1986) BUT IT HAS BEEN PRESENTED AS ILE IN THIS ENTRY. THIS ASSIGNMENT WAS MADE IN THE ORIGINAL ...1: RESIDUE 380 IS LEU IN THE SEQUENCE (K.NAKANO,P.K.HWANG, R.J.FLETTERICK, FEBS LETT., V. 204, P. 283, 1986) BUT IT HAS BEEN PRESENTED AS ILE IN THIS ENTRY. THIS ASSIGNMENT WAS MADE IN THE ORIGINAL STRUCTURE DETERMINATION AT 1.9 ANGSTROMS (PRESENTED IN PROTEIN DATA BANK ENTRY 1GPB) AND CARRIED THROUGH TO THE OTHER ENTRIES. ILE IS MORE CONSISTENT WITH THE ELECTRON DENSITY. HOWEVER, THE RESOLUTION AT 1.9 ANGSTROMS DOES NOT ALLOW A DEFINITIVE ASSIGNMENT. |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 97291.203 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / References: UniProt: P00489, glycogen phosphorylase |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D- ...alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltopentaose |
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#3: Sugar | ChemComp-H2P / |
-Non-polymers , 3 types, 611 molecules
#4: Chemical | ChemComp-PLP / | ||
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#5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Nonpolymer details | MALTOHEPTAOSE CONSISTS OF SEVEN LINKED GLUCOSES. ONLY FIVE OF THE GLUCOSES WERE LOCATED IN THE ...MALTOHEPTA |
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Sequence details | RESIDUE 380 IS LEU IN THE SEQUENCE (K.NAKANO,P.K.HWANG, R.J.FLETTERICK, FEBS LETT., V. 204, P. 283, ...RESIDUE 380 IS LEU IN THE SEQUENCE (K.NAKANO,P.K.HWANG, R.J.FLETTERICK |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.13 % | ||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 16 ℃ / pH: 6.7 / Method: batch method / Details: took Mclaughlin et al., 1984 from original paper | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.86 Å / Num. obs: 18715 / Num. measured all: 88108 / Rmerge(I) obs: 0.063 |
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-Processing
Software | Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.86→8 Å Details: THE N-TERMINAL RESIDUES 14 - 18 WERE ESTABLISHED TOWARDS THE END OF THE REFINEMENT. THESE RESIDUES ARE NOT WELL ORDERED. THEIR ATTACHMENT TO THE REST OF THE CHAIN CONTAINS SOME BAD ...Details: THE N-TERMINAL RESIDUES 14 - 18 WERE ESTABLISHED TOWARDS THE END OF THE REFINEMENT. THESE RESIDUES ARE NOT WELL ORDERED. THEIR ATTACHMENT TO THE REST OF THE CHAIN CONTAINS SOME BAD STEREOCHEMISTRY. A MORE CAREFUL AND CORRECT REPOSITIONING OF THESE RESIDUES IS GIVEN IN PROTEIN DATA BANK ENTRY 2GPB, THE T STATE PHOSPHORYLASE B COMPLEX WITH GLUCOSE.
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Refinement step | Cycle: LAST / Resolution: 2.86→8 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor Rwork: 0.201 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 3.4 |