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- PDB-1aqf: PYRUVATE KINASE FROM RABBIT MUSCLE WITH MG, K, AND L-PHOSPHOLACTATE -

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Basic information

Entry
Database: PDB / ID: 1aqf
TitlePYRUVATE KINASE FROM RABBIT MUSCLE WITH MG, K, AND L-PHOSPHOLACTATE
ComponentsPYRUVATE KINASE
KeywordsTRANSFERASE / PYRUVATE KINASE / RABBIT MUSCLE / DOMAIN MOVEMENT / POTASSIUM BINDING
Function / homologyPyruvate kinase, barrel / Pyruvate kinase, C-terminal / Pyruvate kinase active site signature. / Pyruvate kinase, alpha/beta domain / Pyruvate kinase, barrel domain / Pyruvate kinase, C-terminal domain superfamily / Pyruvate kinase, active site / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / Pyruvate kinase / Pyruvate kinase-like, insert domain superfamily ...Pyruvate kinase, barrel / Pyruvate kinase, C-terminal / Pyruvate kinase active site signature. / Pyruvate kinase, alpha/beta domain / Pyruvate kinase, barrel domain / Pyruvate kinase, C-terminal domain superfamily / Pyruvate kinase, active site / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / Pyruvate kinase / Pyruvate kinase-like, insert domain superfamily / Pyruvate kinase, insert domain superfamily / pyruvate kinase / pyruvate kinase activity / potassium ion binding / kinase activity / magnesium ion binding / ATP binding / nucleus / cytoplasm / Pyruvate kinase PKM
Function and homology information
Specimen sourceOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / 2.7 Å resolution
AuthorsLarsen, T.M. / Benning, M.M. / Wesenberg, G.E. / Rayment, I. / Reed, G.H.
CitationJournal: Arch.Biochem.Biophys. / Year: 1997
Title: Ligand-induced domain movement in pyruvate kinase: structure of the enzyme from rabbit muscle with Mg2+, K+, and L-phospholactate at 2.7 A resolution.
Authors: Larsen, T.M. / Benning, M.M. / Wesenberg, G.E. / Rayment, I. / Reed, G.H.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 29, 1997 / Release: Sep 16, 1998
RevisionDateData content typeGroupProviderType
1.0Sep 16, 1998Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PYRUVATE KINASE
B: PYRUVATE KINASE
C: PYRUVATE KINASE
D: PYRUVATE KINASE
E: PYRUVATE KINASE
F: PYRUVATE KINASE
G: PYRUVATE KINASE
H: PYRUVATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)465,85832
Polyers463,9918
Non-polymers1,86824
Water3,495194
1
A: PYRUVATE KINASE
B: PYRUVATE KINASE
C: PYRUVATE KINASE
D: PYRUVATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,92916
Polyers231,9954
Non-polymers93412
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)19380
ΔGint (kcal/M)-144
Surface area (Å2)73430
MethodPISA
2
E: PYRUVATE KINASE
F: PYRUVATE KINASE
G: PYRUVATE KINASE
H: PYRUVATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,92916
Polyers231,9954
Non-polymers93412
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)18990
ΔGint (kcal/M)-145
Surface area (Å2)69590
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)144.400, 112.600, 171.200
Angle α, β, γ (deg.)90.00, 93.70, 90.00
Int Tables number4
Space group name H-MP 1 21 1

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Components

#1: Protein/peptide
PYRUVATE KINASE /


Mass: 57998.820 Da / Num. of mol.: 8 / Source: (natural) Oryctolagus cuniculus (rabbit) / Genus: Oryctolagus / Tissue: MUSCLE / References: UniProt: P11974, pyruvate kinase
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Formula: K / Potassium
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Formula: Mg / Magnesium
#4: Chemical
ChemComp-PEQ / L-PHOSPHOLACTATE


Mass: 170.058 Da / Num. of mol.: 8 / Formula: C3H7O6P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.99 / Density percent sol: 58.89 %
Crystal grow
*PLUS
pH: 7.5 / Method: batch method
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
17.3 mg/mlenzyme11
27.7 %PEG800011
30.21 M11KCl
45 mM11MgCl2
55 mMATP11
64.5 mML-lactate11
750 mMHEPES11
80.12 mMAp5A11

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Data collection

DiffractionMean temperature: 276 kelvins
DetectorCollection date: Feb 1, 1996
RadiationMonochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
D resolution high: 2.7 Å / D resolution low: 3 Å / Number obs: 76181 / Number measured all: 736673 / Percent possible obs: 94 / Rmerge I obs: 0.075 / Observed criterion sigma I: 3

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Processing

SoftwareName: TNT / Version: 5E / Classification: refinement
RefineSigma F: 0 / Stereochemistry target values: TNT PROTGEO
Least-squares processR factor R work: 0.196 / Highest resolution: 2.7 Å / Lowest resolution: 3 Å / Number reflection obs: 141340 / Percent reflection obs: 93
Refine hist #LASTHighest resolution: 2.7 Å / Lowest resolution: 3 Å
Number of atoms included #LASTProtein: 31209 / Nucleic acid: 0 / Ligand: 96 / Solvent: 194 / Total: 31499
Refine LS restraints
Refine IDTypeDev idealWeight
X-RAY DIFFRACTIONt_bond_d0.014
X-RAY DIFFRACTIONt_angle_deg2.3
X-RAY DIFFRACTIONt_dihedral_angle_d20.553
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes0.0070.012
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd0.015
Software
*PLUS
Version: 5E / Classification: refinement
Least-squares process
*PLUS
R factor obs: 0.196
Refine LS restraints
*PLUS
Refine IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg20.553
X-RAY DIFFRACTIONt_plane_restr0.0070.012

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