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- PDB-1phk: TWO STRUCTURES OF THE CATALYTIC DOMAIN OF PHOSPHORYLASE, KINASE: ... -

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Basic information

Entry
Database: PDB / ID: 1phk
TitleTWO STRUCTURES OF THE CATALYTIC DOMAIN OF PHOSPHORYLASE, KINASE: AN ACTIVE PROTEIN KINASE COMPLEXED WITH NUCLEOTIDE, SUBSTRATE-ANALOGUE AND PRODUCT
ComponentsPHOSPHORYLASE KINASE
KeywordsKINASE / GLYCOGEN METABOLISM / TRANSFERASE / SERINE/THREONINE-PROTEIN / ATP-BINDING / CALMODULIN-BINDING
Function / homology
Function and homology information


phosphorylase kinase / phosphorylase kinase activity / phosphorylase kinase complex / tau-protein kinase / glycogen metabolic process / skeletal muscle myofibril / calmodulin binding / non-specific serine/threonine protein kinase / protein serine kinase activity / ATP binding
Similarity search - Function
Phosphorylase kinase, gamma catalytic subunit / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site ...Phosphorylase kinase, gamma catalytic subunit / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / : / Phosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsOwen, D.J. / Noble, M.E.M. / Garman, E.F. / Papageorgiou, A.C. / Johnson, L.N.
Citation
Journal: Structure / Year: 1995
Title: Two structures of the catalytic domain of phosphorylase kinase: an active protein kinase complexed with substrate analogue and product.
Authors: Owen, D.J. / Noble, M.E. / Garman, E.F. / Papageorgiou, A.C. / Johnson, L.N.
#1: Journal: J.Mol.Biol. / Year: 1995
Title: Expression, Purification and Crystallisation of Phosphorylase Kinase Catalytic Domain
Authors: Owen, D.J. / Papageorgiou, A.C. / Garman, E.F. / Noble, M.E. / Johnson, L.N.
History
DepositionMar 15, 1996Processing site: BNL
Revision 1.0Aug 17, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHOSPHORYLASE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9334
Polymers34,3161
Non-polymers6173
Water2,792155
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.600, 67.400, 110.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PHOSPHORYLASE KINASE / RABBIT MUSCLE PHOSPHORYLASE KINASE


Mass: 34316.297 Da / Num. of mol.: 1 / Fragment: GAMMA SUBUNIT, TRUNCATED TO RESIDUES 1 - 298
Source method: isolated from a genetically manipulated source
Details: LIGANDS ATP AND MN(II) / Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Tissue: SKELETAL MUSCLE / Organ: SKELETAL / Plasmid: PMW172 / Production host: Escherichia coli (E. coli) / References: UniProt: P00518, EC: 2.7.1.38
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 50 %
Crystal grow
*PLUS
Temperature: 14 ℃ / pH: 8.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-12 mg/mlPhk gamma trnc1drop
23 mMAMPPNP1drop
310 mMHEPES/NaOH1drop
42 %(v/v)glycerol1drop
510 mMDTT1drop
60.02 %(w/v)1dropNaN3
70.1 mMEDTA1drop
85 %(w/v)PEG80001reservoir
950 mMHEPES/NaOH1reservoir
1010 mM1reservoirMnCl2
1110 %(v/v)glycerol1reservoir
1210 mMDTT1reservoir
130.02 %(w/v)1reservoirNaN3

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 5, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionHighest resolution: 2.1 Å / Num. obs: 19961 / % possible obs: 88.8 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.074

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
X-PLORphasing
RefinementResolution: 2.2→6 Å / σ(F): 2
RfactorNum. reflection
Rfree0.288 -
Rwork0.21 -
obs0.21 16822
Displacement parametersBiso mean: 47.6 Å2
Refinement stepCycle: LAST / Resolution: 2.2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2229 0 33 155 2417
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.5
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it8
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PHK_AMPPNP_22.ATP_PARPHK_AMPPNP_22.ATP_TOP
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.21 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS

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