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- PDB-1abb: CONTROL OF PHOSPHORYLASE B CONFORMATION BY A MODIFIED COFACTOR: C... -

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Basic information

Entry
Database: PDB / ID: 1abb
TitleCONTROL OF PHOSPHORYLASE B CONFORMATION BY A MODIFIED COFACTOR: CRYSTALLOGRAPHIC STUDIES ON R-STATE GLYCOGEN PHOSPHORYLASE RECONSTITUTED WITH PYRIDOXAL 5'-DIPHOSPHATE
ComponentsGLYCOGEN PHOSPHORYLASE B
KeywordsGLYCOGEN 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
Glycosyl transferase, family 35 / Glycogen/starch/alpha-glucan phosphorylase / Phosphorylase pyridoxal-phosphate attachment site / Carbohydrate phosphorylase / Phosphorylase pyridoxal-phosphate attachment site. / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
INOSINIC ACID / PYRIDOXAL-5'-DIPHOSPHATE / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsLeonidas, 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
DepositionApr 9, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLYCOGEN PHOSPHORYLASE B
B: GLYCOGEN PHOSPHORYLASE B
C: GLYCOGEN PHOSPHORYLASE B
D: GLYCOGEN PHOSPHORYLASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)385,74316
Polymers382,6584
Non-polymers3,08612
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20970 Å2
ΔGint-129 kcal/mol
Surface area112940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.000, 188.100, 88.100
Angle α, β, γ (deg.)90.00, 109.29, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: 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

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Components

#1: Protein
GLYCOGEN PHOSPHORYLASE B


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 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-PDP / PYRIDOXAL-5'-DIPHOSPHATE


Mass: 327.122 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H11NO9P2
#4: Chemical
ChemComp-IMP / INOSINIC ACID


Mass: 348.206 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13N4O8P
Has protein modificationY
Sequence detailsRESIDUE 380 WAS BUILT AS AN ISOLEUCINE AS THIS SIDE CHAIN APPEARED TO FIT THE ELECTRON DENSITY FOR ...RESIDUE 380 WAS BUILT AS AN ISOLEUCINE AS THIS SIDE CHAIN APPEARED TO FIT THE ELECTRON DENSITY FOR THE 1.9 ANGSTROM NATIVE STRUCTURE OF T STATE PHOSPHORYLASE B. HOWEVER, THE SEQUENCE SHOWS THIS TO BE LEUCINE. SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: PHS1_RABIT SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE LEU 380 ILE 380 PRO 609 ALA 609 THE SEQUENCE GIVEN IN THIS ENTRY AGREES WITH THE AMINO ACID SEQUENCE DETERMINED BY TITANI ET AL. (BIOCHEMISTRY, 17, 5680-5693 (1978)) AND WITH THE CDNA SEQUENCE DETERMINED BY NAKANO ET AL. (FEBS LETT. 204:283-287 (1986)).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.41 %
Crystal grow
*PLUS
Temperature: 16 ℃ / pH: 7.5 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein11
21.2-1.4 Mammonium sulfate12
36 mMIMP12
410 mMbeta-glycerophosphate12
50.5 mMEDTA12
63 mMdithiothreitol12
70.02 %12NaN3

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.8 Å / Num. obs: 78049 / % possible obs: 98 % / Num. measured all: 107286 / Rmerge(I) obs: 0.108

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.8→8 Å / σ(F): 1 /
RfactorNum. reflection
Rwork0.21 -
obs0.21 78049
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26772 0 188 0 26960
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg4.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Num. reflection obs: 73340
Solvent computation
*PLUS
Displacement parameters
*PLUS

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