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- PDB-1ayl: PHOSPHOENOLPYRUVATE CARBOXYKINASE -

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Basic information

Entry
Database: PDB / ID: 1ayl
TitlePHOSPHOENOLPYRUVATE CARBOXYKINASE
ComponentsPHOSPHOENOLPYRUVATE CARBOXYKINASE
KeywordsKINASE (TRANSPHOSPHORYLATING) / P-LOOP / PROTEIN-ATP COMPLEX / NUCLEOTIDE-TRIPHOSPHATE HYDROLASE
Function / homologyPhosphoenolpyruvate carboxykinase, N-terminal / Phosphoenolpyruvate carboxykinase, ATP-utilising / Phosphoenolpyruvate carboxykinase, C-terminal / Phosphoenolpyruvate carboxykinase (ATP), conserved site / Phosphoenolpyruvate carboxykinase / Phosphoenolpyruvate carboxykinase (ATP) signature. / phosphoenolpyruvate carboxykinase (ATP) / phosphoenolpyruvate carboxykinase (ATP) activity / gluconeogenesis / calcium ion binding ...Phosphoenolpyruvate carboxykinase, N-terminal / Phosphoenolpyruvate carboxykinase, ATP-utilising / Phosphoenolpyruvate carboxykinase, C-terminal / Phosphoenolpyruvate carboxykinase (ATP), conserved site / Phosphoenolpyruvate carboxykinase / Phosphoenolpyruvate carboxykinase (ATP) signature. / phosphoenolpyruvate carboxykinase (ATP) / phosphoenolpyruvate carboxykinase (ATP) activity / gluconeogenesis / calcium ion binding / magnesium ion binding / ATP binding / cytosol / Phosphoenolpyruvate carboxykinase (ATP)
Function and homology information
Specimen sourceEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 1.8 Å resolution
AuthorsTari, L.W. / Pugazenthi, U. / Goldie, H. / Delbaere, L.T.J.
Citation
Journal: Nat.Struct.Biol. / Year: 1996
Title: Snapshot of an enzyme reaction intermediate in the structure of the ATP-Mg2+-oxalate ternary complex of Escherichia coli PEP carboxykinase.
Authors: Tari, L.W. / Matte, A. / Pugazhenthi, U. / Goldie, H. / Delbaere, L.T.
#1: Journal: To be Published
Title: Allosteric Control by Calcium and Mechanism of Desensitization of Phosphoenolpyruvate Carboxykinase of Escherichia Coli
Authors: Goldie, H. / Sanwal, B.D.
#2: Journal: J.Mol.Biol. / Year: 1996
Title: Crystal Structure of Escherichia Coli Phosphoenolpyruvate Carboxykinase: A New Structural Family with the P-Loop Nucleoside Triphosphate Hydrolase Fold
Authors: Matte, A. / Goldie, H. / Sweet, R.M. / Delbaere, L.T.
#3: Journal: J.Mol.Biol. / Year: 1991
Title: Crystallization of the Calcium-Activated Phosphoenolpyruvate Carboxykinase from Escherichia Coli K12
Authors: Delbaere, L.T. / Vandonselaar, M. / Glaeske, D. / Jabs, C. / Goldie, H.
#4: Journal: J.Bacteriol. / Year: 1990
Title: Sequence of the Pcka Gene of Escherichia Coli K-12: Relevance to Genetic and Allosteric Regulation and Homology of E. Coli Phosphoenolpyruvate Carboxykinase with the Enzymes from Trypanosoma Brucei and Saccharomyces Cerevisiae
Authors: Medina, V. / Pontarollo, R. / Glaeske, D. / Tabel, H. / Goldie, H.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 7, 1995 / Release: Jan 11, 1997
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jan 11, 1997Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelSource and taxonomy / Version format compliance
1.3Nov 29, 2017Structure modelDerived calculations / Otherpdbx_database_status / struct_conf / struct_conf_type_pdbx_database_status.process_site
1.4Mar 21, 2018Structure modelData collectiondiffrn_detector_diffrn_detector.pdbx_collection_date

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHOSPHOENOLPYRUVATE CARBOXYKINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4164
Polyers59,7961
Non-polymers6203
Water6,215345
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)127.510, 96.690, 46.960
Angle α, β, γ (deg.)90.00, 96.63, 90.00
Int Tables number5
Space group name H-MC 1 2 1

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Components

#1: Protein/peptide PHOSPHOENOLPYRUVATE CARBOXYKINASE / / ATP-OXALOACETATE CARBOXY-LYASE (ATP)


Mass: 59796.254 Da / Num. of mol.: 1 / Details: ORDERED MAGNESIUM ION OBSERVED BOUND TO ATP / Source: (natural) Escherichia coli (E. coli) / Genus: Escherichia / Species: Escherichia coli / Strain: K12
References: UniProt: P22259, phosphoenolpyruvate carboxykinase (ATP)
#2: Chemical ChemComp-OXL / OXALATE ION


Mass: 88.019 Da / Num. of mol.: 1 / Formula: C2O4 / Oxalate
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Formula: Mg / Magnesium
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / 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: 2.4 / Density percent sol: 49 %
Crystal grow
*PLUS
Temp: 21 ℃ / pH: 4.4 / Method: vapor diffusion, hanging drop
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
18 mg/mlPCK1drop
22 mMATP1drop
32 mMoxalate1drop
45 mM1dropMgCl2
51 mMEDTA1drop
6100 mMsodium acetate1drop
7200 mMammonium acetate1drop
812 %(w/v)PEG40001drop
9100 mMsodium acetate1reservoir
10200 mMammonium acetate1reservoir
1127 %(w/v)PEG40001reservoir

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Data collection

SourceSource: SYNCHROTRON / Type: PHOTON FACTORY BEAMLINE BL-6B / Synchrotron site: Photon Factory / Beamline: BL-6B / Wavelength: 1
DetectorType: FUJI / Detector: IMAGE PLATE
RadiationMonochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionNumber obs: 40067 / Observed criterion sigma I: 1 / Rmerge I obs: 0.076 / Redundancy: 2.2 % / Percent possible obs: 76.7
Reflection
*PLUS
D resolution high: 1.8 Å

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Processing

Software
NameClassification
X-PLORrefinement
WEISdata reduction
RefineDetails: MET 477 HAS DISALLOWED RAMACHANDRAN ANGLES; THE DEPOSITORS ACCOUNT FOR THIS AS IT IS THE SECOND RESIDUE WITHIN A GAMMA-TURN.
Sigma F: 2
Displacement parametersB iso mean: 21.42 Å2
Least-squares processR factor R free: 0.234 / R factor R work: 0.195 / R factor obs: 0.195 / Highest resolution: 1.8 Å / Lowest resolution: 6 Å / Number reflection obs: 35508
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refine hist #LASTHighest resolution: 1.8 Å / Lowest resolution: 6 Å
Number of atoms included #LASTProtein: 4107 / Nucleic acid: 0 / Ligand: 38 / Solvent: 345 / Total: 4490
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.23
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_deg24.4
X-RAY DIFFRACTIONx_improper_angle_deg1.10

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