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- PDB-1k08: Crystallographic Binding Study of 10 mM N-benzoyl-N'-beta-D-gluco... -

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Basic information

Entry
Database: PDB / ID: 1k08
TitleCrystallographic Binding Study of 10 mM N-benzoyl-N'-beta-D-glucopyranosyl urea to glycogen phosphorylase b
ComponentsGlycogen Phosphorylase
KeywordsTRANSFERASE / glycogen phosphorylase / catalytic site / new allosteric site
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
Chem-BZD / PYRIDOXAL-5'-PHOSPHATE / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.26 Å
AuthorsOikonomakos, N.G. / Kosmopoulou, M. / Zographos, S.E. / Leonidas, D.D. / Chrysina, E.D. / Somsak, L. / Nagy, V. / Praly, J.P. / Docsa, T. / Toth, B. / Gergely, P.
Citation
Journal: Eur.J.Biochem. / Year: 2002
Title: Binding of N-acetyl-N '-beta-D-glucopyranosyl urea and N-benzoyl-N '-beta-D-glucopyranosyl urea to glycogen phosphorylase b: kinetic and crystallographic studies.
Authors: Oikonomakos, N.G. / Kosmopoulou, M. / Zographos, S.E. / Leonidas, D.D. / Chrysina, E.D. / Somsak, L. / Nagy, V. / Praly, J.P. / Docsa, T. / Toth, B. / Gergely, P.
#1: Journal: Structure / Year: 2000
Title: A New Allosteric Site in Glycogen Phosphorylase B as a Target for Drug Interactions
Authors: Oikonomakos, N.G. / Skamnaki, V.T. / Tsitsanou, K.E. / Gavalas, N.G. / Johnson, L.N.
History
DepositionSep 18, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 16, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,1914
Polymers97,2911
Non-polymers9003
Water4,486249
1
A: Glycogen Phosphorylase
hetero molecules

A: Glycogen Phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,3828
Polymers194,5822
Non-polymers1,7996
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area8720 Å2
ΔGint-13 kcal/mol
Surface area57250 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)128.519, 128.519, 116.497
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-1243-

HOH

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Components

#1: Protein Glycogen Phosphorylase / myophosphorylase


Mass: 97291.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: muscle / References: UniProt: P00489, glycogen phosphorylase
#2: Sugar ChemComp-BZD / N-[(phenylcarbonyl)carbamoyl]-beta-D-glucopyranosylamine / N-BENZOYL-N'-BETA-D-GLUCOPYRANOSYL UREA / N-[(phenylcarbonyl)carbamoyl]-beta-D-glucosylamine / N-[(phenylcarbonyl)carbamoyl]-D-glucosylamine / N-[(phenylcarbonyl)carbamoyl]-glucosylamine


Type: D-saccharide / Mass: 326.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H18N2O7
IdentifierTypeProgram
N-benzoyl-N'-b-D-glucopyranosyl ureaIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#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.: 249 / 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: 2.47 Å3/Da / Density % sol: 50.23 %
Crystal growTemperature: 287 K / Method: small tubes / pH: 6.7
Details: BES, EDTA, 10mM N-benzoyl-N'-beta-D-glucopyranosyl urea, pH 6.7, SMALL TUBES, temperature 287K
Crystal grow
*PLUS
Details: Oikonomakos, N.G., (1985) Biochim. Biophys. Acta, 832, 248.

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 2, 2001 / Details: mirrors
RadiationMonochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.26→28.75 Å / Num. all: 44261 / Num. obs: 44361 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 28 Å2 / Rsym value: 9.6 / Net I/σ(I): 10.9
Reflection shellResolution: 2.26→2.3 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 1976 / Rsym value: 42.4 / % possible all: 86.5
Reflection
*PLUS
Num. measured all: 391254 / Rmerge(I) obs: 0.096
Reflection shell
*PLUS
% possible obs: 86.5 % / Rmerge(I) obs: 0.424

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1HLF

1hlf


Resolution: 2.26→28.75 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.212 2247 5.1 %RANDOM
Rwork0.18 ---
all-44199 --
obs-44199 95.8 %-
Displacement parametersBiso mean: 33.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.26→28.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6643 0 61 249 6953
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.72
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.021.5
X-RAY DIFFRACTIONx_mcangle_it3.212
X-RAY DIFFRACTIONx_scbond_it3.652
X-RAY DIFFRACTIONx_scangle_it5.652.5
LS refinement shellResolution: 2.26→2.4 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.336 371 5.4 %
Rwork0.304 6525 -
obs--91.3 %
Software
*PLUS
Name: X-PLOR(ONLINE) / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5.1 % / Rfactor obs: 0.18 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 33.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.72
X-RAY DIFFRACTIONx_mcbond_it2.021.5
X-RAY DIFFRACTIONx_scbond_it3.652
X-RAY DIFFRACTIONx_mcangle_it3.212
X-RAY DIFFRACTIONx_scangle_it5.652.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.336 / % reflection Rfree: 5.4 % / Rfactor Rwork: 0.304

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