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- PDB-1pkm: THE REFINED THREE-DIMENSIONAL STRUCTURE OF CAT MUSCLE (M1) PYRUVA... -

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Basic information

Entry
Database: PDB / ID: 1pkm
TitleTHE REFINED THREE-DIMENSIONAL STRUCTURE OF CAT MUSCLE (M1) PYRUVATE KINASE, AT A RESOLUTION OF 2.6 ANGSTROMS
ComponentsM1 PYRUVATE KINASE
KeywordsKINASE / PYRUVATE KINASE
Function / homology
Function and homology information


pyruvate kinase / pyruvate kinase activity / positive regulation of cytoplasmic translation / positive regulation of sprouting angiogenesis / potassium ion binding / rough endoplasmic reticulum / glycolytic process / cellular response to insulin stimulus / kinase activity / mRNA binding ...pyruvate kinase / pyruvate kinase activity / positive regulation of cytoplasmic translation / positive regulation of sprouting angiogenesis / potassium ion binding / rough endoplasmic reticulum / glycolytic process / cellular response to insulin stimulus / kinase activity / mRNA binding / magnesium ion binding / ATP binding / nucleus / cytoplasm
Similarity search - Function
PK beta-barrel domain-like / M1 Pyruvate Kinase; Domain 3 / Pyruvate kinase, C-terminal domain / Pyruvate Kinase; Chain: A, domain 1 / Pyruvate kinase, active site / Pyruvate kinase active site signature. / Pyruvate kinase / Pyruvate kinase, barrel / Pyruvate kinase, insert domain superfamily / Pyruvate kinase, barrel domain ...PK beta-barrel domain-like / M1 Pyruvate Kinase; Domain 3 / Pyruvate kinase, C-terminal domain / Pyruvate Kinase; Chain: A, domain 1 / Pyruvate kinase, active site / Pyruvate kinase active site signature. / Pyruvate kinase / Pyruvate kinase, barrel / Pyruvate kinase, insert domain superfamily / Pyruvate kinase, barrel domain / Pyruvate kinase, C-terminal / Pyruvate kinase, C-terminal domain superfamily / Pyruvate kinase, alpha/beta domain / Pyruvate kinase-like, insert domain superfamily / Phosphoenolpyruvate-binding domains / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesFelis catus (domestic cat)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsAllen, S.C. / Muirhead, H.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Refined three-dimensional structure of cat-muscle (M1) pyruvate kinase at a resolution of 2.6 A.
Authors: Allen, S.C. / Muirhead, H.
#1: Journal: Embo J. / Year: 1992
Title: The Cooperative Binding of Fructose-1,6-Bisphosphate to Yeast Pyruvate Kinase
Authors: Murcott, T.H.L. / Gutfreund, H. / Muirhead, H.
#2: Journal: Embo J. / Year: 1986
Title: The Structure of Cat Muscle Pyruvate Kinase
Authors: Muirhead, H. / Clayden, D.A. / Barford, D. / Lorimer, C.G. / Fothergill-Gilmore, L.A. / Schiltz, E. / Schmitt, W.
#3: Journal: J.Mol.Biol. / Year: 1979
Title: Crystal Structure of Cat Muscle Pyruvate Kinase at a Resolution of 2.6 Angstroms
Authors: Stuart, D.I. / Levine, M. / Muirhead, H. / Stammers, D.K.
History
DepositionJul 13, 1995Processing site: BNL
Revision 1.0Oct 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Other / Refinement description / Category: pdbx_database_status / software
Item: _pdbx_database_status.process_site / _software.classification
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700SHEET SHEET A IS AN EIGHT-STRANDED PARALLEL BETA-BARREL. SHEET B1 IS A SEVEN-STRANDED PREDOMINANTLY ...SHEET SHEET A IS AN EIGHT-STRANDED PARALLEL BETA-BARREL. SHEET B1 IS A SEVEN-STRANDED PREDOMINANTLY ANTI-PARALLEL BETA-BARREL. TO REPRESENT A BARREL, THE PDB REPEATS THE THE FIRST STRAND AS THE LAST STRAND. SHEET B2 IS FORMED FROM TWO SHORT ANTI-PARALLEL STRANDS. SHEET C IS A TWISTED PREDOMINANTLY PARALLEL FIVE-STRANDED SHEET.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: M1 PYRUVATE KINASE


Theoretical massNumber of molelcules
Total (without water)57,9981
Polymers57,9981
Non-polymers00
Water0
1
A: M1 PYRUVATE KINASE

A: M1 PYRUVATE KINASE

A: M1 PYRUVATE KINASE

A: M1 PYRUVATE KINASE


Theoretical massNumber of molelcules
Total (without water)231,9914
Polymers231,9914
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area16930 Å2
ΔGint-109 kcal/mol
Surface area72120 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)88.400, 115.300, 131.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein M1 PYRUVATE KINASE / PK


Mass: 57997.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Felis catus (domestic cat) / Tissue: MUSCLESkeletal muscle / References: UniProt: P11979, pyruvate kinase

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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: 2.88 Å3/Da / Density % sol: 57.24 %
Crystal grow
*PLUS
pH: 6 / Method: unknown / Details: Stammers, D.K., (1975) J. Mol. Biol., 95, 213.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
113-17 mg/mlprotein11
250 %satammonium sulfate12
320 mMsodium phosphate12

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Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: FILM / Detector: FILM / Date: Jan 1, 1978
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 15441 / % possible obs: 74 % / Rmerge(I) obs: 0.05
Reflection
*PLUS
Num. obs: 15440 / Rmerge(I) obs: 0.05

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Processing

Software
NameClassification
X-PLORmodel building
TNTrefinement
X-PLORrefinement
MOSCOdata reduction
3DSCALEdata reduction
X-PLORphasing
RefinementResolution: 2.6→10 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.175 -
obs-15441
Refinement stepCycle: LAST / Resolution: 2.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3976 0 0 0 3976
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.69
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_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Lowest resolution: 6 Å / Num. reflection obs: 15440 / Rfactor obs: 0.175
Solvent computation
*PLUS
Displacement parameters
*PLUS

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