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- PDB-8f6m: Complex of Rabbit muscle pyruvate kinase with ADP and the phospho... -

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Basic information

Entry
Database: PDB / ID: 8f6m
TitleComplex of Rabbit muscle pyruvate kinase with ADP and the phosphonate analogue of PEP mimicking the Michaelis complex.
ComponentsPyruvate kinase PKM
KeywordsCYTOSOLIC PROTEIN / glycolysis / metabolic kinase / central metabolism
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 / non-specific protein-tyrosine kinase / cellular response to insulin stimulus / protein tyrosine kinase activity / non-specific serine/threonine protein kinase ...pyruvate kinase / pyruvate kinase activity / positive regulation of cytoplasmic translation / positive regulation of sprouting angiogenesis / potassium ion binding / rough endoplasmic reticulum / non-specific protein-tyrosine kinase / cellular response to insulin stimulus / protein tyrosine kinase activity / non-specific serine/threonine protein kinase / phosphorylation / mRNA binding / magnesium ion binding / ATP binding / nucleus
Similarity search - Function
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 ...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 / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ALANINE / (E)-2-METHYL-3-PHOSPHONOACRYLATE / : / : / SUCCINIC ACID / Pyruvate kinase PKM
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsHolyoak, T. / Fenton, A.W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Database (Oxford) / Year: 2023
Title: PYK-SubstitutionOME: an integrated database containing allosteric coupling, ligand affinity and mutational, structural, pathological, bioinformatic and computational information about pyruvate kinase isozymes.
Authors: Swint-Kruse, L. / Dougherty, L.L. / Page, B. / Wu, T. / O'Neil, P.T. / Prasannan, C.B. / Timmons, C. / Tang, Q. / Parente, D.J. / Sreenivasan, S. / Holyoak, T. / Fenton, A.W.
History
DepositionNov 16, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyruvate kinase PKM
B: Pyruvate kinase PKM
C: Pyruvate kinase PKM
D: Pyruvate kinase PKM
E: Pyruvate kinase PKM
F: Pyruvate kinase PKM
G: Pyruvate kinase PKM
H: Pyruvate kinase PKM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)473,37486
Polymers464,9128
Non-polymers8,46178
Water51,9192882
1
A: Pyruvate kinase PKM
F: Pyruvate kinase PKM
G: Pyruvate kinase PKM
H: Pyruvate kinase PKM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,49442
Polymers232,4564
Non-polymers4,03838
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26030 Å2
ΔGint-154 kcal/mol
Surface area68790 Å2
MethodPISA
2
B: Pyruvate kinase PKM
C: Pyruvate kinase PKM
D: Pyruvate kinase PKM
E: Pyruvate kinase PKM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,88044
Polymers232,4564
Non-polymers4,42440
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28130 Å2
ΔGint-169 kcal/mol
Surface area67720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.026, 216.396, 258.151
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Pyruvate kinase PKM / Pyruvate kinase muscle isozyme / Threonine-protein kinase PKM2 / Tyrosine-protein kinase PKM2


Mass: 58114.016 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
References: UniProt: P11974, pyruvate kinase, non-specific serine/threonine protein kinase, non-specific protein-tyrosine kinase

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Non-polymers , 8 types, 2960 molecules

#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C4H6O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: Mn
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#6: Chemical
ChemComp-ALA / ALANINE / Alanine


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H7NO2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical
ChemComp-GZ3 / (E)-2-METHYL-3-PHOSPHONOACRYLATE


Mass: 166.069 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H7O5P / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2882 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.79 Å3/Da / Density % sol: 55.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 15 mM succinate, 50 mM KCl, 19 to 24% PEG 8,000 well solution

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 12, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.15→100 Å / Num. obs: 545313 / % possible obs: 100 % / Redundancy: 3.7 % / Biso Wilson estimate: 22.67 Å2 / Rmerge(I) obs: 0.127 / Χ2: 1.083 / Net I/σ(I): 7.9 / Num. measured all: 2026691
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.15-2.233.70.583545851.1341100
2.23-2.323.70.47545591.1721100
2.32-2.423.70.386544781.0861100
2.42-2.553.70.319545031.0661100
2.55-2.713.70.245545571.0311100
2.71-2.923.70.182545121.0661100
2.92-3.213.80.125545981.0491100
3.21-3.683.80.082544811.0091100
3.68-4.633.80.068545821.1121100
4.63-1003.70.046544581.106199.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G50

2g50


Resolution: 2.15→46.02 Å / SU ML: 0.2071 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.4323
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2047 14171 5.05 %
Rwork0.1559 266503 -
obs0.1584 280674 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.33 Å2
Refinement stepCycle: LAST / Resolution: 2.15→46.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31753 0 498 2882 35133
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01332878
X-RAY DIFFRACTIONf_angle_d1.11244361
X-RAY DIFFRACTIONf_chiral_restr0.06535051
X-RAY DIFFRACTIONf_plane_restr0.01025737
X-RAY DIFFRACTIONf_dihedral_angle_d9.60794676
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.180.26454770.19838525X-RAY DIFFRACTION96.74
2.18-2.20.26014860.19038803X-RAY DIFFRACTION99.86
2.2-2.230.24695190.18248758X-RAY DIFFRACTION99.86
2.23-2.260.24324660.18398790X-RAY DIFFRACTION99.91
2.26-2.290.2265000.17528815X-RAY DIFFRACTION99.88
2.29-2.320.23654560.178808X-RAY DIFFRACTION99.87
2.32-2.350.22874590.16928835X-RAY DIFFRACTION99.86
2.35-2.390.24474600.17138855X-RAY DIFFRACTION99.82
2.39-2.420.2464840.17198757X-RAY DIFFRACTION99.85
2.42-2.460.24444610.16728858X-RAY DIFFRACTION99.87
2.46-2.510.22215020.16178819X-RAY DIFFRACTION99.88
2.51-2.550.22054640.16318795X-RAY DIFFRACTION99.8
2.55-2.60.23034870.1578824X-RAY DIFFRACTION99.91
2.6-2.650.21224820.15288882X-RAY DIFFRACTION99.91
2.65-2.710.21934530.15658835X-RAY DIFFRACTION99.85
2.71-2.770.21574690.15678865X-RAY DIFFRACTION99.86
2.77-2.840.21584700.1558833X-RAY DIFFRACTION99.82
2.84-2.920.21154620.15378892X-RAY DIFFRACTION99.88
2.92-3.010.21914720.1498894X-RAY DIFFRACTION99.86
3.01-3.10.20194330.14948943X-RAY DIFFRACTION99.91
3.1-3.210.20054600.14718874X-RAY DIFFRACTION99.94
3.21-3.340.19124760.15048873X-RAY DIFFRACTION99.9
3.34-3.50.18184550.1448929X-RAY DIFFRACTION99.98
3.5-3.680.2054650.14548950X-RAY DIFFRACTION99.96
3.68-3.910.19084760.14228948X-RAY DIFFRACTION99.9
3.91-4.210.16494730.13698979X-RAY DIFFRACTION99.93
4.21-4.640.15154550.13039001X-RAY DIFFRACTION99.89
4.64-5.310.18554920.15269018X-RAY DIFFRACTION99.97
5.31-6.680.22224640.1849142X-RAY DIFFRACTION99.95
6.68-46.020.18134930.16379403X-RAY DIFFRACTION99.54
Refinement TLS params.Method: refined / Origin x: -68.880740931 Å / Origin y: 8.69493851476 Å / Origin z: 71.2736044974 Å
111213212223313233
T0.150351848485 Å20.0110577271136 Å2-0.0293890501183 Å2-0.166785603689 Å20.00509971061099 Å2--0.185253342871 Å2
L0.0529881839073 °20.0208344203609 °2-0.0303567776502 °2-0.0668008553849 °2-0.0454466772042 °2--0.130150644923 °2
S0.00718167619503 Å °-0.00893411178208 Å °0.00381952026185 Å °0.00623138258176 Å °-0.0137936341631 Å °-0.0102758159855 Å °-0.0125870846165 Å °0.0200285555363 Å °0.00712844885432 Å °
Refinement TLS groupSelection details: all

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