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- PDB-1p2d: Crystal Structure of Glycogen Phosphorylase B in complex with Bet... -

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Basic information

Entry
Database: PDB / ID: 1p2d
TitleCrystal Structure of Glycogen Phosphorylase B in complex with Beta Cyclodextrin
ComponentsGlycogen phosphorylase, muscle form
KeywordsTRANSFERASE
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
alpha-maltose / PYRIDOXAL-5'-PHOSPHATE / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.94 Å
AuthorsPinotsis, N. / Leonidas, D.D. / Chrysina, E.D. / Oikonomakos, N.G. / Mavridis, I.M.
CitationJournal: Protein Sci. / Year: 2003
Title: The binding of beta- and gamma-cyclodextrins to glycogen phosphorylase b: Kinetic and crystallographic studies.
Authors: Pinotsis, N. / Leonidas, D.D. / Chrysina, E.D. / Oikonomakos, N.G. / Mavridis, I.M.
History
DepositionApr 15, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 2, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_source / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,8813
Polymers97,2911
Non-polymers5892
Water5,837324
1
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,7616
Polymers194,5822
Non-polymers1,1794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area6680 Å2
ΔGint-4 kcal/mol
Surface area57130 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)128.873, 128.873, 116.179
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1321-

HOH

DetailsTHIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. COORDINATES FOR A COMPLETE DIMER REPRESENTING THE KNOWN BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE MOLECULE CAN BE GENERATED BY APPLYING THE TWO FOLD AXIS : y,x,1-z

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Components

#1: Protein Glycogen phosphorylase, muscle form / Glycogen Phosphorylase B


Mass: 97291.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P00489, glycogen phosphorylase
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.37 %
Crystal growTemperature: 289 K / Method: small tubes / pH: 6.7 / Details: BES, EDTA, pH 6.7, SMALL TUBES, temperature 289K
Crystal grow
*PLUS
pH: 6.7 / Method: unknown
Details: Oikonomakos, N.G., (2000) J.Biol.Chem., 275, 34566.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
125 mg/mlenzyme11
21 mMflavopiridol11
33 mMdithiothreitol11
410 mMBes11
50.1 mMEDTA11
60.02 %sodium azide11
71 mMspermine11or 10 mM magnesium acetate
850 mMglucose11

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8068 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 22, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8068 Å / Relative weight: 1
ReflectionResolution: 1.94→30 Å / Num. all: 68504 / Num. obs: 68504 / % possible obs: 93.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.4 % / Biso Wilson estimate: 17.9 Å2 / Rsym value: 0.076 / Net I/σ(I): 13.3
Reflection shellResolution: 1.94→1.96 Å / Mean I/σ(I) obs: 2.1 / Rsym value: 0.499 / % possible all: 85
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 714419 / Rmerge(I) obs: 0.076
Reflection shell
*PLUS
% possible obs: 85 % / Rmerge(I) obs: 0.499

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345data collection
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1GFZ

1gfz


Resolution: 1.94→29.51 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3573624.95 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.218 3462 5.1 %RANDOM
Rwork0.193 ---
obs0.193 68011 93.6 %-
all-68011 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.2621 Å2 / ksol: 0.380243 e/Å3
Displacement parametersBiso mean: 29.7 Å2
Baniso -1Baniso -2Baniso -3
1-2.96 Å20 Å20 Å2
2--2.96 Å20 Å2
3----5.92 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 1.94→29.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6581 0 37 324 6942
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.31.5
X-RAY DIFFRACTIONc_mcangle_it2.012
X-RAY DIFFRACTIONc_scbond_it2.132
X-RAY DIFFRACTIONc_scangle_it3.282.5
LS refinement shellResolution: 1.94→2.06 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.292 510 4.7 %
Rwork0.253 10438 -
obs--91.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PLP.PARAMPLP.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4BCD.PARAMBCD.TOP
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79

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