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- PDB-1aq2: PHOSPHOENOLPYRUVATE CARBOXYKINASE -

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Basic information

Entry
Database: PDB / ID: 1aq2
TitlePHOSPHOENOLPYRUVATE CARBOXYKINASE
ComponentsPHOSPHOENOLPYRUVATE CARBOXYKINASE
KeywordsKINASE / TRANSPHOSPHORYLATING / P-LOOP / PROTEIN-ATP COMPLEX / NUCLEOTIDE-TRIPHOSPHATE HYDROLASE / LYASE / GLUCONEOGENESIS
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 / MOLECULAR REPLACEMENT / 1.9 Å resolution
AuthorsTari, L.W. / Matte, A. / Goldie, H. / Delbaere, L.T.J.
Citation
Journal: Nat.Struct.Biol. / Year: 1997
Title: Mg(2+)-Mn2+ clusters in enzyme-catalyzed phosphoryl-transfer reactions.
Authors: Tari, L.W. / Matte, A. / Goldie, H. / Delbaere, L.T.
#1: 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.
#2: 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.
#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: Aug 5, 1997 / Release: Oct 14, 1998
RevisionDateData content typeGroupCategoryItemProviderType
1.0Oct 14, 1998Structure 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
1.4Apr 18, 2018Structure modelData collectiondiffrn_detector_diffrn_detector.detector

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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)60,3845
Polyers59,7091
Non-polymers6744
Water4,179232
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)126.190, 96.610, 46.860
Angle α, β, γ (deg.)90.00, 95.80, 90.00
Int Tables number5
Space group name H-MC 1 2 1

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Components

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Protein/peptide , 1 types, 1 molecules A

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


Mass: 59709.176 Da / Num. of mol.: 1
Details: ORDERED MAGNESIUM AND MANGANESE IONS OBSERVED BOUND TO ATP
Source: (gene. exp.) Escherichia coli (E. coli) / Genus: Escherichia / Species: Escherichia coli / Strain: K12
Description: NATIVE PROMOTER OF E. COLI PCKA GENE, HIGHLY AEROBIC GROWTH TO EARLY STATIONARY PHASE IN THE ABSENCE OF CARBOHYDRATES
Cellular location: CYTOPLASM / Genus (production host): Escherichia / Gene (production host): PCKA / Production host: Escherichia coli (E. coli)
References: UniProt: P22259, phosphoenolpyruvate carboxykinase (ATP)

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Non-polymers , 5 types, 236 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Formula: Mn / Manganese
#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: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 1 / Formula: C3H4O3 / Pyruvic acid
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.38 / Density percent sol: 50 %
Crystal growpH: 4.4 / Details: pH 4.4

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Data collection

DiffractionMean temperature: 300 kelvins
SourceType: ENRAF-NONIUS / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Collection date: Oct 15, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionD resolution high: 1.9 Å / D resolution low: 6 Å / Number obs: 39324 / Observed criterion sigma I: 1 / Rsym value: 0.118 / NetI over sigmaI: 4.3 / Redundancy: 2.6 % / Percent possible obs: 90
Reflection shellHighest resolution: 1.9 Å / Lowest resolution: 3 Å / MeanI over sigI obs: 2.1 / Rsym value: 0.34 / Redundancy: 2.4 % / Percent possible all: 85

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
MADNESdata reduction
CCP4data scaling
X-PLORphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AYL
Cross valid method: FREE-R / Sigma F: 2
Least-squares processR factor R free: 0.26 / R factor R work: 0.218 / R factor obs: 0.218 / Highest resolution: 1.9 Å / Lowest resolution: 6 Å / Number reflection R free: 1907 / Number reflection obs: 37529 / Percent reflection R free: 5
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refine hist #LASTHighest resolution: 1.9 Å / Lowest resolution: 6 Å
Number of atoms included #LASTProtein: 4114 / Nucleic acid: 0 / Ligand: 39 / Solvent: 232 / Total: 4385
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.32
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

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