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- PDB-7r6y: E117K mutant pyruvate kinase from rabbit muscle -

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Basic information

Entry
Database: PDB / ID: 7r6y
TitleE117K mutant pyruvate kinase from rabbit muscle
ComponentsPyruvate kinase PKM
KeywordsTRANSFERASE / Mutant / Magnesium / oxalate / pyruvate kinase / PK
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
ACETATE ION / OXALATE ION / Pyruvate kinase PKM
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsRodriguez-Romero, A. / Rodriguez-Hernandez, A.
Funding support Mexico, 1items
OrganizationGrant numberCountry
Consejo Nacional de Ciencia y Tecnologia (CONACYT)087163 Mexico
CitationJournal: Int J Mol Sci / Year: 2022
Title: The K + -Dependent and -Independent Pyruvate Kinases Acquire the Active Conformation by Different Mechanisms.
Authors: Ramirez-Silva, L. / Hernandez-Alcantara, G. / Guerrero-Mendiola, C. / Gonzalez-Andrade, M. / Rodriguez-Romero, A. / Rodriguez-Hernandez, A. / Lugo-Munguia, A. / Gomez-Coronado, P.A. / ...Authors: Ramirez-Silva, L. / Hernandez-Alcantara, G. / Guerrero-Mendiola, C. / Gonzalez-Andrade, M. / Rodriguez-Romero, A. / Rodriguez-Hernandez, A. / Lugo-Munguia, A. / Gomez-Coronado, P.A. / Rodriguez-Mendez, C. / Vega-Segura, A.
History
DepositionJun 24, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,50121
Polymers232,5204
Non-polymers98117
Water11,494638
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.340, 121.830, 161.370
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 12 through 24 or (resid 25...
d_2ens_1(chain "B" and ((resid 12 and (name N or name...
d_1ens_2(chain "C" and ((resid 11 through 12 and (name N...
d_2ens_2(chain "D" and (resid 11 through 26 or (resid 27...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ILELEUA1 - 15
d_12ens_1HISARGA18 - 515
d_13ens_1VALPROA519 - 522
d_21ens_1ILELEUB1 - 15
d_22ens_1HISARGB19 - 516
d_23ens_1VALPROB518 - 521
d_11ens_2PHELYSC1 - 107
d_12ens_2ASPPROC123 - 437
d_21ens_2PHEPROD1 - 422

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.253958369339, -0.247716290992, 0.93495549938), (-0.256899808098, -0.949201728396, -0.181710119173), (0.932473932741, -0.194043082813, -0.304695990735)-5.41983905111, 75.1776504099, 27.5328481837
2given(0.271154385073, -0.229567240319, 0.934758889569), (-0.216465514599, -0.960808985671, -0.173172671178), (0.937879512755, -0.155386534892, -0.310220960493)-6.53789831057, 73.9306397823, 26.4224440899

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Components

#1: Protein
Pyruvate kinase PKM / Pyruvate kinase muscle isozyme


Mass: 58130.078 Da / Num. of mol.: 4 / Mutation: E117K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: PKM, PKM2 / Production host: Escherichia coli (E. coli) / References: UniProt: P11974, pyruvate kinase
#2: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-OXL / OXALATE ION / Oxalate


Mass: 88.019 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2O4
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 638 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.29 Å3/Da / Density % sol: 46.29 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion
Details: 0.2 M magnesium acetate, 0.1 M sodium cacodylate pH 6.5, and 18% w/v Polyethylene Glycol 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 23, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.25→48.18 Å / Num. obs: 101836 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 31.62 Å2 / CC1/2: 0.99 / Net I/σ(I): 17.5
Reflection shellResolution: 2.25→2.37 Å / Num. unique obs: 14698 / CC1/2: 0.81

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1aqf

1aqf


Resolution: 2.25→44.97 Å / SU ML: 0.2931 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.046
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2496 4987 4.9 %
Rwork0.2009 96743 -
obs0.2033 101730 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.12 Å2
Refinement stepCycle: LAST / Resolution: 2.25→44.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14288 0 64 638 14990
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006114587
X-RAY DIFFRACTIONf_angle_d0.89819710
X-RAY DIFFRACTIONf_chiral_restr0.0552276
X-RAY DIFFRACTIONf_plane_restr0.00632577
X-RAY DIFFRACTIONf_dihedral_angle_d17.99982043
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.595644924711
ens_2d_2CX-RAY DIFFRACTIONTorsion NCS0.525515176074
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.280.3181830.28033167X-RAY DIFFRACTION99.94
2.28-2.30.31861680.25353191X-RAY DIFFRACTION99.91
2.3-2.330.32661660.25453167X-RAY DIFFRACTION100
2.33-2.360.30681590.25133189X-RAY DIFFRACTION100
2.36-2.390.29871570.24513216X-RAY DIFFRACTION100
2.39-2.420.31851620.24663172X-RAY DIFFRACTION100
2.42-2.460.3151530.24963219X-RAY DIFFRACTION100
2.46-2.490.2961730.23693191X-RAY DIFFRACTION99.97
2.49-2.530.31911640.23493184X-RAY DIFFRACTION99.97
2.53-2.580.28041640.23813212X-RAY DIFFRACTION100
2.58-2.620.32641510.2263199X-RAY DIFFRACTION100
2.62-2.670.2831610.22033212X-RAY DIFFRACTION100
2.67-2.720.27081600.2153204X-RAY DIFFRACTION100
2.72-2.770.26621730.21983212X-RAY DIFFRACTION99.97
2.77-2.830.27591780.21863184X-RAY DIFFRACTION100
2.83-2.90.29681770.21933190X-RAY DIFFRACTION100
2.9-2.970.24511750.22233203X-RAY DIFFRACTION100
2.97-3.050.26351600.21923208X-RAY DIFFRACTION100
3.05-3.140.27991770.21453223X-RAY DIFFRACTION100
3.14-3.240.26421510.21293215X-RAY DIFFRACTION100
3.24-3.360.25111860.2033213X-RAY DIFFRACTION100
3.36-3.50.23421830.18543208X-RAY DIFFRACTION100
3.5-3.650.22851530.18543239X-RAY DIFFRACTION100
3.65-3.850.20631470.17883264X-RAY DIFFRACTION100
3.85-4.090.2291690.16513246X-RAY DIFFRACTION100
4.09-4.40.20631760.16033252X-RAY DIFFRACTION100
4.4-4.850.18781570.15523276X-RAY DIFFRACTION100
4.85-5.550.22831560.17953305X-RAY DIFFRACTION100
5.55-6.980.20271580.19913337X-RAY DIFFRACTION100
6.98-44.970.241900.19623445X-RAY DIFFRACTION99.56

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