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- PDB-1a5u: PYRUVATE KINASE COMPLEX WITH BIS MG-ATP-NA-OXALATE -

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Basic information

Entry
Database: PDB / ID: 1a5u
TitlePYRUVATE KINASE COMPLEX WITH BIS MG-ATP-NA-OXALATE
ComponentsPYRUVATE KINASE
KeywordsTRANSFERASE / PYRUVATE KINASE
Function / homologyPyruvate kinase, barrel / Pyruvate kinase, C-terminal / Pyruvate kinase active site signature. / Pyruvate kinase, alpha/beta domain / Pyruvate kinase, barrel domain / Pyruvate kinase-like domain superfamily / Pyruvate kinase, C-terminal domain superfamily / Pyruvate kinase, active site / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / Pyruvate kinase ...Pyruvate kinase, barrel / Pyruvate kinase, C-terminal / Pyruvate kinase active site signature. / Pyruvate kinase, alpha/beta domain / Pyruvate kinase, barrel domain / Pyruvate kinase-like domain superfamily / 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 / positive regulation of sprouting angiogenesis / kinase activity / magnesium ion binding / ATP binding / nucleus / cytoplasm / Pyruvate kinase PKM
Function and homology information
Specimen sourceOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 2.35 Å resolution
AuthorsLarsen, T.M. / Benning, M.M. / Rayment, I. / Reed, G.H.
CitationJournal: Biochemistry / Year: 1998
Title: Structure of the bis(Mg2+)-ATP-oxalate complex of the rabbit muscle pyruvate kinase at 2.1 A resolution: ATP binding over a barrel.
Authors: Larsen, T.M. / Benning, M.M. / Rayment, I. / Reed, G.H.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 18, 1998 / Release: Mar 2, 1999
RevisionDateData content typeGroupProviderType
1.0Mar 2, 1999Structure 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)468,26244
Polyers463,9918
Non-polymers4,27136
Water32,6071810
1
A: PYRUVATE KINASE
B: PYRUVATE KINASE
C: PYRUVATE KINASE
D: PYRUVATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,13122
Polyers231,9954
Non-polymers2,13618
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)22010
ΔGint (kcal/M)-207
Surface area (Å2)70360
MethodPISA
2
E: PYRUVATE KINASE
F: PYRUVATE KINASE
G: PYRUVATE KINASE
H: PYRUVATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,13122
Polyers231,9954
Non-polymers2,13618
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)22120
ΔGint (kcal/M)-212
Surface area (Å2)70200
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)95.300, 216.500, 258.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP 21 21 21

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Components

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Protein/peptide , 1 types, 8 molecules ABCDEFGH

#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

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Non-polymers , 5 types, 1846 molecules

#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Formula: Na / Sodium
#3: Chemical
ChemComp-OXL / OXALATE ION


Mass: 88.019 Da / Num. of mol.: 8 / Formula: C2O4 / Oxalate
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 14 / Formula: Mg / Magnesium
#5: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 6 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1810 / Formula: H2O / Water

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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: 2.74 / Density percent sol: 57.2 %
Crystal growpH: 6 / Details: pH 6.0
Crystal grow
*PLUS
Method: batch method
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
17.1 mg/mlprotein11
27.8 %PEG800011
30.16 M11NaCl
45 mM11MgCl2
55 mMATP11
61 mMoxalate11
750 mMsuccinic11

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Data collection

DiffractionMean temperature: 113
SourceSource: SYNCHROTRON / Type: SSRL BEAMLINE BL7-1 / Synchrotron site: SSRL / Beamline: BL7-1
DetectorCollection date: May 1, 1996
RadiationMonochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionD resolution high: 2.35 / D resolution low: 30 / Number obs: 193413 / Percent possible obs: 90
Reflection shellHighest resolution: 2.35 / Lowest resolution: 2.46 / Rsym value: 0.19 / Percent possible all: 74
Reflection
*PLUS
Number all: 216128 / Number measured all: 717630 / Rmerge I obs: 0.053
Reflection shell
*PLUS
Percent possible obs: 74 / Rmerge I obs: 0.164

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Processing

Software
NameVersionClassification
AMoREphasing
TNT5Drefinement
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AQF
Least-squares processR factor R work: 0.19 / Highest resolution: 2.35 / Lowest resolution: 30 / Percent reflection obs: 85
Refine hist #LASTHighest resolution: 2.35 / Lowest resolution: 30
Number of atoms included #LASTProtein: 31824 / Nucleic acid: 0 / Ligand: 256 / Solvent: 1810 / Total: 33890
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.013
X-RAY DIFFRACTIONt_angle_deg2.1
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Version: 5D / Classification: refinement
Least-squares process
*PLUS
R factor obs: 0.19

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