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- PDB-2pxz: E. coli phosphoenolpyruvate carboxykinase (PEPCK) complexed with ... -

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Basic information

Entry
Database: PDB / ID: 2pxz
TitleE. coli phosphoenolpyruvate carboxykinase (PEPCK) complexed with ATP, Mg2+, Mn2+, carbon dioxide and oxaloacetate
ComponentsPhosphoenolpyruvate carboxykinase
KeywordsLYASE / p-loop / oxaloacetate / carbon dioxide / CO2
Function / homology
Function and homology information


phosphoenolpyruvate carboxykinase (ATP) / phosphoenolpyruvate carboxykinase (ATP) activity / gluconeogenesis / calcium ion binding / magnesium ion binding / ATP binding / cytosol
Similarity search - Function
Phosphoenolpyruvate carboxykinase, ATP-utilising / Phosphoenolpyruvate carboxykinase (ATP), conserved site / Phosphoenolpyruvate carboxykinase / Phosphoenolpyruvate carboxykinase (ATP) signature. / Phosphoenolpyruvate Carboxykinase; domain 2 / Phosphoenolpyruvate Carboxykinase, domain 2 / Phosphoenolpyruvate Carboxykinase; domain 1 / Phosphoenolpyruvate Carboxykinase, domain 1 / Phosphoenolpyruvate Carboxykinase; domain 3 - #20 / Phosphoenolpyruvate carboxykinase, C-terminal ...Phosphoenolpyruvate carboxykinase, ATP-utilising / Phosphoenolpyruvate carboxykinase (ATP), conserved site / Phosphoenolpyruvate carboxykinase / Phosphoenolpyruvate carboxykinase (ATP) signature. / Phosphoenolpyruvate Carboxykinase; domain 2 / Phosphoenolpyruvate Carboxykinase, domain 2 / Phosphoenolpyruvate Carboxykinase; domain 1 / Phosphoenolpyruvate Carboxykinase, domain 1 / Phosphoenolpyruvate Carboxykinase; domain 3 - #20 / Phosphoenolpyruvate carboxykinase, C-terminal / Phosphoenolpyruvate carboxykinase, N-terminal / Phosphoenolpyruvate Carboxykinase; domain 3 / Beta Complex / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / CARBON DIOXIDE / : / OXALOACETATE ION / Phosphoenolpyruvate carboxykinase (ATP)
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsDelbaere, L.T.J. / Cotelesage, J.J.H. / Goldie, H.
CitationJournal: To be Published
Title: Crystal structure of E. coli phosphoenolpyruvate carboxykinase (PEPCK) complexed with ATP, Mg2+, Mn2+, carbon dioxide and oxaloacetate
Authors: Delbaere, L.T.J. / Cotelesage, J.J.H. / Goldie, H.
History
DepositionMay 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Phosphoenolpyruvate carboxykinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4716
Polymers59,7091
Non-polymers7615
Water5,098283
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.556, 94.302, 46.354
Angle α, β, γ (deg.)90.00, 95.54, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules X

#1: Protein Phosphoenolpyruvate carboxykinase / PEP carboxykinase / Phosphoenolpyruvate carboxylase / PEPCK


Mass: 59709.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: pckA / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K12
References: UniProt: P22259, phosphoenolpyruvate carboxykinase (ATP)

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Non-polymers , 6 types, 288 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-OAA / OXALOACETATE ION


Mass: 131.064 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H3O5
#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#6: Chemical ChemComp-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / Source method: isolated from a natural source / Formula: H2O

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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: 2.27 Å3/Da / Density % sol: 45.77 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 8ul drop with 8ug/ml protein, 2mM ADP, 5mM MgCl2, 10 uM MnCl2, 1 mM EDTA, 100 mM sodium acetate (pH 4.4), 200 mM ammonium acetate and 12% w/v PEG 4000 was allowed to equilibrate with a 1 ml ...Details: 8ul drop with 8ug/ml protein, 2mM ADP, 5mM MgCl2, 10 uM MnCl2, 1 mM EDTA, 100 mM sodium acetate (pH 4.4), 200 mM ammonium acetate and 12% w/v PEG 4000 was allowed to equilibrate with a 1 ml reservoir of 100 mM sodium aceate, 200 mM ammonium acetate and 27% PEG 4000. After crystals grew for one week 2ul of a 1 mM EDTA and saturated sodium oxaloacetate solution was added to the drop. 5 ul of glycerol was added to the drop. A 0.1 x 0.1 x 0.3 mm crystal was removed with a loop and flash cooled in liquid nitrogen, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.3317 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationMonochromator: Diamond (111) double-crystal monochromator Bent cylindrical Si-mirror (Rh coating)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3317 Å / Relative weight: 1
ReflectionResolution: 1.83→47.14 Å / Num. all: 595228 / Num. obs: 171743 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 13.2 / Redundancy: 3.6 % / Rsym value: 0.085
Reflection shellResolution: 2.23→2.28 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 24303 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.23→38.32 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.902 / SU B: 5.689 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R: 0.297 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23421 1322 5 %RANDOM
Rwork0.17277 ---
obs0.17585 24889 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.323 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20.01 Å2
2---0.04 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.23→38.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4007 0 45 283 4335
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0224144
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9321.9585646
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0255524
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.04924.19179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.91415625
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5911521
X-RAY DIFFRACTIONr_chiral_restr0.1430.2631
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023176
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.210.21908
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.22817
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2293
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.240.233
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3740.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0471.52689
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.65324172
X-RAY DIFFRACTIONr_scbond_it2.76731694
X-RAY DIFFRACTIONr_scangle_it4.0494.51474
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.225→2.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 97 -
Rwork0.179 1834 -
obs--100 %

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