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- PDB-1bx3: EFFECTS OF COMMONLY USED CRYOPROTECTANTS ON GLYCOGEN PHOSPHORYLAS... -

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Basic information

Entry
Database: PDB / ID: 1bx3
TitleEFFECTS OF COMMONLY USED CRYOPROTECTANTS ON GLYCOGEN PHOSPHORYLASE ACTIVITY AND STRUCTURE
ComponentsPROTEIN (GLYCOGEN PHOSPHORYLASE B)
KeywordsTRANSFERASE / PHOSPHORYLASE / INHIBITOR / CRYOPROTECTANT / MPD / DMSO / CRYOCRYSTALLOGRAPHY
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
PYRIDOXAL-5'-PHOSPHATE / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.3 Å
AuthorsTsitsanou, K.E. / Oikonomakos, N.G. / Zographos, S.E. / Skamnaki, V.T. / Gregoriou, M. / Watson, K.A. / Johnson, L.N. / Fleet, G.W.J.
Citation
Journal: Protein Sci. / Year: 1999
Title: Effects of commonly used cryoprotectants on glycogen phosphorylase activity and structure.
Authors: Tsitsanou, K.E. / Oikonomakos, N.G. / Zographos, S.E. / Skamnaki, V.T. / Gregoriou, M. / Watson, K.A. / Johnson, L.N. / Fleet, G.W.
#1: Journal: Glycogen Phosphorylase B: Description of the Protein Structure
Year: 1991
Title: Glycogen Phosphorylase B: Description of the Protein Structure
Authors: Acharya, K.R. / Stuart, D.I. / Varvill, K.M. / Johnson, L.N.
History
DepositionOct 13, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 21, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (GLYCOGEN PHOSPHORYLASE B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,5382
Polymers97,2911
Non-polymers2471
Water12,124673
1
A: PROTEIN (GLYCOGEN PHOSPHORYLASE B)
hetero molecules

A: PROTEIN (GLYCOGEN PHOSPHORYLASE B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,0774
Polymers194,5822
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)126.040, 126.040, 115.190
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-1633-

HOH

21A-1634-

HOH

31A-1643-

HOH

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Components

#1: Protein PROTEIN (GLYCOGEN PHOSPHORYLASE B)


Mass: 97291.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: SCHIFF'S BASE LINK BETWEEN PLP AND LYS 680 / Source: (natural) Oryctolagus cuniculus (rabbit) / Cellular location: CYTOPLASM / Tissue: MUSCLE / References: UniProt: P00489, glycogen phosphorylase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


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


Mass: 18.015 Da / Num. of mol.: 673 / 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: 2.35 Å3/Da / Density % sol: 47.66 %
Crystal growTemperature: 289 K / pH: 6.7
Details: THE PROTEIN WAS CRYSTALLIZED FROM 0.01 M BES, PH 6.7, 0.003 M DTT, 0.001 M SPERMINE, 0.0001 M EDTA, 0.02 % (W/V) SODIUM AZIDE AT 16 DEGREES C. THE CRYSTALS WERE CRYOPROTECTED WITH 30% (V/V) ...Details: THE PROTEIN WAS CRYSTALLIZED FROM 0.01 M BES, PH 6.7, 0.003 M DTT, 0.001 M SPERMINE, 0.0001 M EDTA, 0.02 % (W/V) SODIUM AZIDE AT 16 DEGREES C. THE CRYSTALS WERE CRYOPROTECTED WITH 30% (V/V) DMSO (DIMETHYLSULFOXIDE)., temperature 289K
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: unknown
Details: Oikonomakos, N.G., (1985) Biochim.Biophys.Acta., 832, 248.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
127.5 mg/mlphosphorylase b11
21.1 mMIMP11
31.1 mMspermine11
410 mMBes11
52.9 mMdithiothreitol11
60.1 mMEDTA11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.928
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 29, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.928 Å / Relative weight: 1
ReflectionResolution: 2.3→36.8 Å / Num. obs: 41713 / % possible obs: 99.9 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 20.59
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 0.103 / Mean I/σ(I) obs: 10.48 / % possible all: 99.5
Reflection
*PLUS
Num. measured all: 244996
Reflection shell
*PLUS
% possible obs: 99.5 %

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Processing

Software
NameVersionClassification
CCP4model building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: OTHER
Starting model: PDB ENTRY 2GPN

2gpn


Resolution: 2.3→36.8 Å / Cross valid method: FREE R-FACTOR / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.252 2107 5 %RANDOM
Rwork0.186 ---
obs0.186 41713 99.9 %-
Refinement stepCycle: LAST / Resolution: 2.3→36.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6519 0 15 673 7207
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.2
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

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