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- PDB-2gpn: 100 K STRUCTURE OF GLYCOGEN PHOSPHORYLASE AT 2.0 ANGSTROMS RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 2gpn
Title100 K STRUCTURE OF GLYCOGEN PHOSPHORYLASE AT 2.0 ANGSTROMS RESOLUTION
ComponentsGLYCOGEN PHOSPHORYLASE B
KeywordsGLYCOGEN PHOSPHORYLASE / WATER STRUCTURE / 100 K X-RAY STRUCTURE / MPD / TRANSFERASE
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
Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER / Resolution: 1.99 Å
AuthorsGregoriou, M. / Noble, M.E.M. / Watson, K.A. / Garman, E.F. / Krulle, T.M. / De La Fuente, C. / Fleet, G.W.J. / Oikonomakos, N.G. / Johnson, L.N.
Citation
Journal: Protein Sci. / Year: 1998
Title: The structure of a glycogen phosphorylase glucopyranose spirohydantoin complex at 1.8 A resolution and 100 K: the role of the water structure and its contribution to binding.
Authors: Gregoriou, M. / Noble, M.E. / Watson, K.A. / Garman, E.F. / Krulle, T.M. / de la Fuente, C. / Fleet, G.W. / Oikonomakos, N.G. / Johnson, L.N.
History
DepositionMar 26, 1998Processing site: BNL
Revision 1.0Jul 1, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLYCOGEN PHOSPHORYLASE B


Theoretical massNumber of molelcules
Total (without water)97,5191
Polymers97,5191
Non-polymers00
Water14,718817
1
A: GLYCOGEN PHOSPHORYLASE B

A: GLYCOGEN PHOSPHORYLASE B


Theoretical massNumber of molelcules
Total (without water)195,0392
Polymers195,0392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area3870 Å2
ΔGint-19 kcal/mol
Surface area56230 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)127.180, 127.180, 115.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein GLYCOGEN PHOSPHORYLASE B


Mass: 97519.320 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 817 / 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: 2.4 Å3/Da / Density % sol: 48.7 %
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 25% (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 25% (V/V) MPD (2-METHYL-2,4-PENTANEDIOL)., temperature 289K
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
127-28 mg/mlprotein11
21 mMspermine11
310 mMBES11
43 mMdithiothreitol11
50.1 mMEDTA11
60.02 %sodium azide11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 19, 1996 / Details: MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.99→19.4 Å / Num. obs: 57703 / % possible obs: 89.7 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 10.1
Reflection shellResolution: 1.99→2.14 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 2.1 / % possible all: 89.5
Reflection
*PLUS
Num. measured all: 192914
Reflection shell
*PLUS
% possible obs: 89.5 %

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Processing

Software
NameClassification
CCP4model building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: AN UNPUBLISHED 1.5 ANGSTROMS MODEL (E.P.MITCHELL) AND PDB ENTRY 1GPB

1gpb


Resolution: 1.99→19.4 Å / Cross valid method: FREE R-FACTOR
RfactorNum. reflection% reflectionSelection details
Rfree0.248 2862 5 %RANDOM
Rwork0.197 ---
obs-54841 89.7 %-
Refine analyzeLuzzati sigma a obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 1.99→19.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6546 0 0 817 7363
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Num. reflection all: 57703 / Rfactor all: 0.248 / Rfactor obs: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.008
X-RAY DIFFRACTIONp_angle_deg1.5

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