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- PDB-1l5r: Human liver glycogen phosphorylase a complexed with riboflavin, N... -

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Basic information

Entry
Database: PDB / ID: 1l5r
TitleHuman liver glycogen phosphorylase a complexed with riboflavin, N-Acetyl-beta-D-Glucopyranosylamine and CP-403,700
Componentsglycogen phosphorylase, liver form
KeywordsTRANSFERASE / phosphorylase / purine site
Function / homology
Function and homology information


vitamin binding / purine nucleobase binding / 5-phosphoribose 1-diphosphate biosynthetic process / glucose binding / glycogen phosphorylase / glycogen phosphorylase activity / linear malto-oligosaccharide phosphorylase activity / SHG alpha-glucan phosphorylase activity / glycogen catabolic process / bile acid binding ...vitamin binding / purine nucleobase binding / 5-phosphoribose 1-diphosphate biosynthetic process / glucose binding / glycogen phosphorylase / glycogen phosphorylase activity / linear malto-oligosaccharide phosphorylase activity / SHG alpha-glucan phosphorylase activity / glycogen catabolic process / bile acid binding / glycogen metabolic process / Glycogen breakdown (glycogenolysis) / AMP binding / necroptotic process / response to bacterium / pyridoxal phosphate binding / glucose homeostasis / secretory granule lumen / ficolin-1-rich granule lumen / Neutrophil degranulation / extracellular exosome / extracellular region / ATP binding / identical protein binding / cytosol / cytoplasm
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-700 / N-acetyl-beta-D-glucopyranosylamine / PYRIDOXAL-5'-PHOSPHATE / RIBOFLAVIN / Glycogen phosphorylase, liver form
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsEkstrom, J.L. / Pauly, T.A. / Carty, M.D. / Soeller, W.C. / Culp, J. / Danley, D.E. / Hoover, D.J. / Treadway, J.L. / Gibbs, E.M. / Fletterick, R.J. ...Ekstrom, J.L. / Pauly, T.A. / Carty, M.D. / Soeller, W.C. / Culp, J. / Danley, D.E. / Hoover, D.J. / Treadway, J.L. / Gibbs, E.M. / Fletterick, R.J. / Day, Y.S.N. / Myszka, D.G. / Rath, V.L.
CitationJournal: Chem.Biol. / Year: 2002
Title: Structure-activity analysis of the purine binding site of human liver glycogen phosphorylase.
Authors: Ekstrom, J.L. / Pauly, T.A. / Carty, M.D. / Soeller, W.C. / Culp, J. / Danley, D.E. / Hoover, D.J. / Treadway, J.L. / Gibbs, E.M. / Fletterick, R.J. / Day, Y.S. / Myszka, D.G. / Rath, V.L.
History
DepositionMar 7, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3May 2, 2012Group: Structure summary
Revision 1.4Jul 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.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Remark 999 SEQUENCE THE NUMBERING OF THE SEQUENCE IS SHIFTED BY ONE IN AGREEMENT WITH THE CONVENTION IN THE ... SEQUENCE THE NUMBERING OF THE SEQUENCE IS SHIFTED BY ONE IN AGREEMENT WITH THE CONVENTION IN THE LITERATURE FOR THIS PROTEIN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: glycogen phosphorylase, liver form
B: glycogen phosphorylase, liver form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,1898
Polymers194,5532
Non-polymers1,6366
Water9,854547
1
A: glycogen phosphorylase, liver form
B: glycogen phosphorylase, liver form
hetero molecules

A: glycogen phosphorylase, liver form
B: glycogen phosphorylase, liver form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)392,37816
Polymers389,1064
Non-polymers3,27212
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z+1/31
Unit cell
Length a, b, c (Å)124.422, 124.422, 124.006
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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Protein / Sugars , 2 types, 3 molecules AB

#1: Protein glycogen phosphorylase, liver form / / Glycogen phosphorylase a


Mass: 97276.469 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ: liver / Production host: Escherichia coli (E. coli) / References: UniProt: P06737, glycogen phosphorylase
#2: Sugar ChemComp-NBG / N-acetyl-beta-D-glucopyranosylamine


Type: D-saccharide / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
b-D-Glcp1NAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 5 types, 552 molecules

#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Chemical ChemComp-700 / [5-CHLORO-1H-INDOL-2-CARBONYL-PHENYLALANINYL]-AZETIDINE-3-CARBOXYLIC ACID / CP403700 / (S)-1-{2-[(5-CHLORO-1H-INDOLE-2-CARBONYL)-AMINO]-3-PHENYL-PROPIONYL}-AZETIDINE-3-CARBOXYLATE


Mass: 425.865 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H20ClN3O4
#5: Chemical ChemComp-RBF / RIBOFLAVIN / RIBOFLAVINE / VITAMIN B2 / Riboflavin


Mass: 376.364 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H20N4O6
#6: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 547 / 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: 2.85 Å3/Da / Density % sol: 56.8 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6
Details: MES, MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Temperature: 17 ℃ / pH: 6.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
125-30 mg/mlprotein1drop
220 mMsodium BES1droppH6.8
31 mMEDTA1drop
40.5 mMdithiothreitol1drop
50.1 Msodium MES1reservoirpH6.0
625-35 %MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.95 Å
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Feb 8, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.1→99 Å / Num. all: 368381 / Num. obs: 361382 / % possible obs: 98.1 % / Observed criterion σ(I): -2 / Redundancy: 3 % / Biso Wilson estimate: 21 Å2 / Rsym value: 0.092 / Net I/σ(I): 11.4
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 11928 / Rsym value: 0.418 / % possible all: 95.3
Reflection
*PLUS
Lowest resolution: 99 Å / Num. obs: 122788 / Redundancy: 2.9 % / Num. measured all: 368381 / Rmerge(I) obs: 0.092
Reflection shell
*PLUS
% possible obs: 95.3 % / Rmerge(I) obs: 0.418

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
CNS1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→55.61 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 151125.78 / Data cutoff high rms absF: 151125.78 / 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
Rfree0.283 11972 10 %RANDOM
Rwork0.247 ---
obs0.247 119714 95.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.8381 Å2 / ksol: 0.341542 e/Å3
Displacement parametersBiso mean: 35.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å21.61 Å20 Å2
2---0.77 Å20 Å2
3---1.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.1→55.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12840 0 110 547 13497
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_mcangle_it1.882
X-RAY DIFFRACTIONc_scbond_it1.792
X-RAY DIFFRACTIONc_scangle_it2.472.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.354 1773 9.8 %
Rwork0.308 16366 -
obs--86.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ALL2.PARALL2.TOP
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 99 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86

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