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- PDB-8f5t: Rabbit muscle pyruvate kinase in complex with sodium and magnesium -

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Basic information

Entry
Database: PDB / ID: 8f5t
TitleRabbit muscle pyruvate kinase in complex with sodium and magnesium
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 / protein tyrosine kinase activity / non-specific serine/threonine protein kinase / phosphorylation ...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 / 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
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 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 15, 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)466,30033
Polymers464,9128
Non-polymers1,38825
Water28,2111566
1
A: Pyruvate kinase PKM
B: Pyruvate kinase PKM
C: Pyruvate kinase PKM
D: Pyruvate kinase PKM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,07416
Polymers232,4564
Non-polymers61812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18450 Å2
ΔGint-161 kcal/mol
Surface area72960 Å2
MethodPISA
2
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)233,22617
Polymers232,4564
Non-polymers77013
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18900 Å2
ΔGint-151 kcal/mol
Surface area72900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.453, 113.759, 169.144
Angle α, β, γ (deg.)90.000, 94.050, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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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 / Details: S-->A substitution an naturally occurring variant / 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 , 5 types, 1591 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1566 / 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: 2.94 Å3/Da / Density % sol: 58.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 50 mM Tris 50 mM NaCl and a range of 7.5 to 10% PEG 20,000

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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: 2.4→50 Å / Num. obs: 397612 / % possible obs: 97.4 % / Redundancy: 2.2 % / Biso Wilson estimate: 38.64 Å2 / Rmerge(I) obs: 0.09 / Χ2: 1.073 / Net I/σ(I): 10.9 / Num. measured all: 870606
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.4-2.4920.478385561.075194.3
2.49-2.5920.386388161.074195.1
2.59-2.72.10.303391751.016195.8
2.7-2.852.10.231393461.049196.6
2.85-3.022.10.173397351.055197.3
3.02-3.262.20.124399621.061197.9
3.26-3.582.30.092401201.046198.3
3.58-4.12.30.073405251.092199.2
4.1-5.172.40.069408191.075199.9
5.17-502.30.041405581.163199.4

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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: 2.41→47.16 Å / SU ML: 0.3167 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.7672
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2318 10347 5.04 %
Rwork0.1848 194988 -
obs0.1872 205335 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.79 Å2
Refinement stepCycle: LAST / Resolution: 2.41→47.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31859 0 82 1566 33507
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002332425
X-RAY DIFFRACTIONf_angle_d0.50343746
X-RAY DIFFRACTIONf_chiral_restr0.04375010
X-RAY DIFFRACTIONf_plane_restr0.00345670
X-RAY DIFFRACTIONf_dihedral_angle_d13.497612243
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.41-2.430.33612710.27935299X-RAY DIFFRACTION80.58
2.43-2.460.32553360.27026446X-RAY DIFFRACTION97.3
2.46-2.490.32163370.26646368X-RAY DIFFRACTION97.09
2.49-2.520.31893670.25476411X-RAY DIFFRACTION97.78
2.52-2.560.33340.24386403X-RAY DIFFRACTION97.67
2.56-2.590.30393530.23846398X-RAY DIFFRACTION98
2.59-2.630.30743590.23826488X-RAY DIFFRACTION98.14
2.63-2.670.28233630.23196394X-RAY DIFFRACTION98.4
2.67-2.710.28363600.2256518X-RAY DIFFRACTION98.6
2.71-2.760.2783340.21546486X-RAY DIFFRACTION98.67
2.76-2.80.28543540.22066488X-RAY DIFFRACTION98.62
2.8-2.850.29123400.22916524X-RAY DIFFRACTION98.93
2.85-2.910.30863380.23196562X-RAY DIFFRACTION99.04
2.91-2.970.293280.22726497X-RAY DIFFRACTION99.24
2.97-3.030.2773340.21836552X-RAY DIFFRACTION99.49
3.03-3.10.28963480.20726556X-RAY DIFFRACTION99.32
3.1-3.180.26823550.21036555X-RAY DIFFRACTION99.44
3.18-3.270.28063530.20476540X-RAY DIFFRACTION99.49
3.27-3.360.25183560.20276568X-RAY DIFFRACTION99.6
3.36-3.470.2473140.19026571X-RAY DIFFRACTION99.48
3.47-3.60.21663270.18226598X-RAY DIFFRACTION99.64
3.6-3.740.22643340.17366622X-RAY DIFFRACTION99.87
3.74-3.910.20873830.16516570X-RAY DIFFRACTION99.84
3.91-4.120.18213570.15756588X-RAY DIFFRACTION99.93
4.12-4.370.173520.14496647X-RAY DIFFRACTION99.99
4.37-4.710.17283600.13626610X-RAY DIFFRACTION99.99
4.71-5.180.19653460.15286642X-RAY DIFFRACTION99.99
5.18-5.930.21523430.16936662X-RAY DIFFRACTION99.89
5.93-7.470.20783510.1686684X-RAY DIFFRACTION99.86
7.47-47.160.16193600.13786741X-RAY DIFFRACTION99.07
Refinement TLS params.Method: refined / Origin x: 101.303674017 Å / Origin y: -33.3469151033 Å / Origin z: 78.7644914441 Å
111213212223313233
T0.249482174672 Å20.0046929905566 Å20.0201718181889 Å2-0.214737641051 Å2-0.0313268261722 Å2--0.248835037059 Å2
L0.132940492989 °2-0.018111501227 °20.0720007917678 °2-0.0499753303106 °2-0.0698795651948 °2--0.186956363897 °2
S0.0045890728328 Å °-0.0510561519596 Å °0.00366858114013 Å °0.00507071515325 Å °-0.00532782648199 Å °-0.00159471599972 Å °-0.0223940866171 Å °0.00871342429888 Å °0.00150449748181 Å °
Refinement TLS groupSelection details: all

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