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- PDB-1p4h: Crystal structure of glycogen phosphorylase b in complex with C-(... -

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Basic information

Entry
Database: PDB / ID: 1p4h
TitleCrystal structure of glycogen phosphorylase b in complex with C-(1-acetamido-alpha-D-glucopyranosyl) formamide
ComponentsGlycogen phosphorylase, muscle form
KeywordsTRANSFERASE
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
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
Chem-CR6 / PYRIDOXAL-5'-PHOSPHATE / PHOSPHATE ION / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.06 Å
AuthorsChrysina, E.D. / Oikonomakos, N.G. / Zographos, S.E. / Kosmopoulou, M.N. / Bischler, N. / Leonidas, D.D. / Nagy, V. / Somsak, L. / Gergely, P. / Praly, J.-P.
CitationJournal: Biocatal.Biotransfor. / Year: 2003
Title: Crsytallographic Studies on alpha- and beta-D-glucopyranosyl Formamide Analogues, Inhibitors of Glycogen Phosphorylase
Authors: Chrysina, E.D. / Oikonomakos, N.G. / Zographos, S.E. / Kosmopoulou, M.N. / Bischler, N. / Leonidas, D.D. / Kovacs, L. / Docsa, T. / Gergely, P. / Somsak, L.
History
DepositionApr 23, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 18, 2004Provider: 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 1.4Jul 29, 2020Group: Data collection / Derived calculations
Category: diffrn_source / struct_conn ...diffrn_source / struct_conn / struct_site / struct_site_gen
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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)97,8984
Polymers97,2911
Non-polymers6063
Water5,747319
1
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,7958
Polymers194,5822
Non-polymers1,2136
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area7070 Å2
ΔGint-21 kcal/mol
Surface area55660 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)127.980, 127.980, 115.529
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe biological assembly is a dimer generated from the monomer in the asymmetric unit by the operation: y,x,1-z

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Components

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


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: Sugar ChemComp-CR6 / 1-DEOXY-1-ACETYLAMINO-BETA-D-GLUCO-2-HEPTULOPYRANOSONAMIDE


Type: D-saccharide / Mass: 264.233 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C9H16N2O7
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


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


Mass: 18.015 Da / Num. of mol.: 319 / 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: 2.43 Å3/Da / Density % sol: 49.39 %
Crystal growTemperature: 289 K / Method: small tubes / pH: 6.7 / Details: BES, EDTA, pH 6.7, SMALL TUBES, temperature 289K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8015 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 31, 2003
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8015 Å / Relative weight: 1
ReflectionResolution: 2.06→30 Å / Num. all: 59423 / Num. obs: 59423 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 28.1 Å2 / Rsym value: 0.083 / Net I/σ(I): 17.1
Reflection shellResolution: 2.06→2.1 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 2723 / Rsym value: 0.565 / % possible all: 92.8

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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: 2.06→29.98 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3607438.54 / 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
Rfree0.205 3004 5.1 %RANDOM
Rwork0.185 ---
obs0.185 59358 99.3 %-
all-59538 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.5334 Å2 / ksol: 0.308428 e/Å3
Displacement parametersBiso mean: 33.9 Å2
Baniso -1Baniso -2Baniso -3
1-3.42 Å20 Å20 Å2
2--3.42 Å20 Å2
3----6.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.06→29.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6585 0 38 319 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_d22
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_mcbond_it1.231.5
X-RAY DIFFRACTIONc_mcangle_it1.982
X-RAY DIFFRACTIONc_scbond_it2.062
X-RAY DIFFRACTIONc_scangle_it3.22.5
LS refinement shellResolution: 2.06→2.19 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.299 478 5 %
Rwork0.282 8994 -
obs--96.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN_DEMETRES.TOP
X-RAY DIFFRACTION2PLP.PARAMPLP.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4GLA.PARAMGLA.TOP
X-RAY DIFFRACTION5PHOSPHATE.PARAMFPP.TOP

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