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- PDB-1z0n: the glycogen-binding domain of the AMP-activated protein kinase -

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Basic information

Entry
Database: PDB / ID: 1z0n
Titlethe glycogen-binding domain of the AMP-activated protein kinase
Components5'-AMP-activated protein kinase, beta-1 subunit
KeywordsSUGAR BINDING PROTEIN / beta sandwich
Function / homology
Function and homology information


Energy dependent regulation of mTOR by LKB1-AMPK / Regulation of TP53 Activity through Phosphorylation / Macroautophagy / TP53 Regulates Metabolic Genes / nail development / nucleotide-activated protein kinase complex / cellular response to nutrient levels / fatty acid biosynthetic process / positive regulation of cold-induced thermogenesis / protein kinase activity ...Energy dependent regulation of mTOR by LKB1-AMPK / Regulation of TP53 Activity through Phosphorylation / Macroautophagy / TP53 Regulates Metabolic Genes / nail development / nucleotide-activated protein kinase complex / cellular response to nutrient levels / fatty acid biosynthetic process / positive regulation of cold-induced thermogenesis / protein kinase activity / positive regulation of gene expression / protein kinase binding / signal transduction / protein-containing complex / nucleus / cytosol / cytoplasm
Similarity search - Function
Association with the SNF1 complex (ASC) domain / ASC domain superfamily / : / 5'-AMP-activated protein kinase beta subunit, interaction domain / 5'-AMP-activated protein kinase beta subunit, interation domain / AMP-activated protein kinase, glycogen-binding domain / Glycogen recognition site of AMP-activated protein kinase / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like fold ...Association with the SNF1 complex (ASC) domain / ASC domain superfamily / : / 5'-AMP-activated protein kinase beta subunit, interaction domain / 5'-AMP-activated protein kinase beta subunit, interation domain / AMP-activated protein kinase, glycogen-binding domain / Glycogen recognition site of AMP-activated protein kinase / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
beta-cyclodextrin / 5'-AMP-activated protein kinase subunit beta-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.49 Å
AuthorsPolekhina, G. / Gupta, A. / van Denderen, B.J. / Feil, S.C. / Kemp, B.E. / Stapleton, D. / Parker, M.W.
Citation
Journal: Structure / Year: 2005
Title: Structural Basis for Glycogen Recognition by AMP-Activated Protein Kinase.
Authors: Polekhina, G. / Gupta, A. / van Denderen, B.J. / Feil, S.C. / Kemp, B.E. / Stapleton, D. / Parker, M.W.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2005
Title: Crystallization of the glycogen-binding domain of the AMP-activated protein kinase beta subunit and preliminary X-ray analysis
Authors: Polekhina, G. / Feil, S.C. / Gupta, A. / O'Donnell, P. / Stapleton, D. / Parker, M.W.
History
DepositionMar 2, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_validate_chiral / pdbx_validate_close_contact / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_atom_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_seq_id_1
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 10, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-AMP-activated protein kinase, beta-1 subunit
B: 5'-AMP-activated protein kinase, beta-1 subunit
C: 5'-AMP-activated protein kinase, beta-1 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3786
Polymers32,9193
Non-polymers3,4593
Water5,531307
1
A: 5'-AMP-activated protein kinase, beta-1 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1262
Polymers10,9731
Non-polymers1,1531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 5'-AMP-activated protein kinase, beta-1 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1262
Polymers10,9731
Non-polymers1,1531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 5'-AMP-activated protein kinase, beta-1 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1262
Polymers10,9731
Non-polymers1,1531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.750, 45.250, 50.600
Angle α, β, γ (deg.)71.90, 69.70, 65.40
Int Tables number1
Space group name H-MP1

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Components

#1: Protein 5'-AMP-activated protein kinase, beta-1 subunit / AMPK beta-1 chain / AMPKb / 40 kDa subunit


Mass: 10973.046 Da / Num. of mol.: 3 / Fragment: 68-163 fragment / Mutation: L105M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pProEX HT / Production host: Escherichia coli (E. coli) / Strain (production host): Novagen 834 (DE3) / References: UniProt: P80386
#2: Polysaccharide Cycloheptakis-(1-4)-(alpha-D-glucopyranose) / beta-cyclodextrin


Type: oligosaccharide, Oligosaccharide / Class: Drug delivery / Mass: 1153.001 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: cyclic oligosaccharide / References: beta-cyclodextrin
DescriptorTypeProgram
WURCS=2.0/1,7,7/[a2122h-1a_1-5]/1-1-1-1-1-1-1/a1-g4_a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1WURCSPDB2Glycan 1.1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 2.3 Å3/Da / Density % sol: 51.65 %
Crystal growTemperature: 299 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG, monomethyl ether 5000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 299K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.9791 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 10, 2004
RadiationMonochromator: Diamond (111) double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.48→24 Å / Num. all: 23738 / Num. obs: 23738 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.049 / Χ2: 1.111
Reflection shellResolution: 1.48→1.51 Å / % possible obs: 91.4 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.332 / Num. measured obs: 3324 / Χ2: 0.458 / % possible all: 91.4

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Phasing

PhasingMethod: MIR

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
CNSrefinement
REFMAC5.2.0005refinement
PDB_EXTRACT1.6data extraction
DMphasing
RefinementMethod to determine structure: MIR / Resolution: 1.49→23.27 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.247 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21256 2583 5.1 %RANDOM
Rwork0.18388 ---
all0.18534 23738 --
obs0.184 23738 96.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.137 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20.31 Å2-1.06 Å2
2---0.38 Å2-0.3 Å2
3---1.21 Å2
Refinement stepCycle: LAST / Resolution: 1.49→23.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1992 0 231 307 2530
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222304
X-RAY DIFFRACTIONr_angle_refined_deg1.6662.0473171
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.835244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.45424.563103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.34515323
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.55159
X-RAY DIFFRACTIONr_chiral_restr0.2050.2399
X-RAY DIFFRACTIONr_gen_planes_refined0.0420.021732
X-RAY DIFFRACTIONr_nbd_refined0.2280.2956
X-RAY DIFFRACTIONr_nbtor_refined0.3180.21597
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2254
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.278
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.237
X-RAY DIFFRACTIONr_mcbond_it2.04131265
X-RAY DIFFRACTIONr_mcangle_it2.99742000
X-RAY DIFFRACTIONr_scbond_it1.65221176
X-RAY DIFFRACTIONr_scangle_it2.2853.51171
LS refinement shellResolution: 1.49→1.529 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 197 -
Rwork0.297 3486 -
obs--94.27 %

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