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- PDB-1z8d: Crystal Structure of Human Muscle Glycogen Phosphorylase a with A... -

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Basic information

Entry
Database: PDB / ID: 1z8d
TitleCrystal Structure of Human Muscle Glycogen Phosphorylase a with AMP and Glucose
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 / Glycogen breakdown (glycogenolysis) / glycogen metabolic process / pyridoxal phosphate binding / nucleotide binding / extracellular exosome ...glycogen phosphorylase / glycogen phosphorylase activity / linear malto-oligosaccharide phosphorylase activity / SHG alpha-glucan phosphorylase activity / glycogen catabolic process / Glycogen breakdown (glycogenolysis) / glycogen metabolic process / pyridoxal phosphate binding / nucleotide binding / extracellular exosome / 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
ADENINE / ADENOSINE MONOPHOSPHATE / alpha-D-glucopyranose / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLukacs, C.M. / Oikonomakos, N.G. / Crowther, R.L. / Hong, L.N. / Kammlott, R.U. / Levin, W. / Li, S. / Liu, C.M. / Lucas-McGady, D. / Pietranico, S. / Reik, L.
CitationJournal: Proteins / Year: 2006
Title: The crystal structure of human muscle glycogen phosphorylase a with bound glucose and AMP: An intermediate conformation with T-state and R-state features.
Authors: Lukacs, C.M. / Oikonomakos, N.G. / Crowther, R.L. / Hong, L.N. / Kammlott, R.U. / Levin, W. / Li, S. / Liu, C.M. / Lucas-McGady, D. / Pietranico, S. / Reik, L.
History
DepositionMar 30, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / 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 1.4Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)98,1954
Polymers97,5321
Non-polymers6633
Water6,648369
1
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,3898
Polymers195,0642
Non-polymers1,3256
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area9600 Å2
ΔGint-26 kcal/mol
Surface area56340 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)92.370, 144.000, 59.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe second molecule of the biological assembly is generated by the operation 1-x, -y, z

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Components

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


Mass: 97532.117 Da / Num. of mol.: 1 / Mutation: S14(SEP), K680(LLP)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PYGM / Plasmid: pFASTBAC / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf9 / References: UniProt: P11217, glycogen phosphorylase
#2: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical ChemComp-ADE / ADENINE / Adenine


Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 369 / 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: 2.1 Å3/Da / Density % sol: 40.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: PEG mme 550, glucose, TRIS, spermine, DTT, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 5, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.28→76.7 Å / Num. all: 36521 / Num. obs: 36521 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 11.9 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 11.4
Reflection shellResolution: 2.28→2.36 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.201 / Mean I/σ(I) obs: 5 / Num. unique all: 3434 / % possible all: 93.1

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Processing

Software
NameVersionClassification
CNX2000.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 7GPB

7gpb


Resolution: 2.3→30.79 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 3316479 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.251 706 2 %RANDOM
Rwork0.192 ---
all-35334 --
obs-35334 98.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.4752 Å2 / ksol: 0.382354 e/Å3
Displacement parametersBiso mean: 17.3 Å2
Baniso -1Baniso -2Baniso -3
1-3.95 Å20 Å20 Å2
2---1.38 Å20 Å2
3----2.57 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.3→30.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6707 0 45 369 7121
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_d21.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.141.5
X-RAY DIFFRACTIONc_mcangle_it1.742
X-RAY DIFFRACTIONc_scbond_it1.912
X-RAY DIFFRACTIONc_scangle_it2.712.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.311 107 1.8 %
Rwork0.218 5734 -
obs--98.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION4AMP.PARAMAMP.TOP

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