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- PDB-6com: 2.3A crystal structure of E. coli phosphoenolpyruvate carboxykina... -

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Basic information

Entry
Database: PDB / ID: 6com
Title2.3A crystal structure of E. coli phosphoenolpyruvate carboxykinase mutant Asp269Asn
ComponentsPhosphoenolpyruvate carboxykinase (ATP)
KeywordsLYASE / enzyme / Pepcarboxykinase
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 / PYRUVIC ACID / Phosphoenolpyruvate carboxykinase (ATP)
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSokaribo, A.S. / Cotelesage, J.H. / Novakovski, B. / Goldie, H. / Sanders, D.
CitationJournal: Biochim Biophys Acta Gen Subj / Year: 2020
Title: Kinetic and structural analysis of Escherichia coli phosphoenolpyruvate carboxykinase mutants.
Authors: Sokaribo, A. / Novakovski, B.A.A. / Cotelesage, J. / White, A.P. / Sanders, D. / Goldie, H.
History
DepositionMar 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Structure summary / Category: citation / citation_author / struct
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct.title
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoenolpyruvate carboxykinase (ATP)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3685
Polymers59,7081
Non-polymers6604
Water5,405300
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)124.595, 94.175, 46.457
Angle α, β, γ (deg.)90.000, 94.770, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-984-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Phosphoenolpyruvate carboxykinase (ATP) / PEPCK


Mass: 59708.191 Da / Num. of mol.: 1 / Mutation: D269N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: pckA, pck, b3403, JW3366 / Production host: Escherichia coli (E. coli)
References: UniProt: P22259, phosphoenolpyruvate carboxykinase (ATP)

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Non-polymers , 5 types, 304 molecules

#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 2.33 Å3/Da / Density % sol: 47.24 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 8.2
Details: A 2ul drop with 2 mg/ml protein, 5 mM Calcium chloride, 5mM Magnesium chloride, 2 mM ATP, 2mM Pyruvate, 1 mM EDTA, 200 mM Ammonium acetate, 100 mM Sodium acetate, 0.01 mM DTT, 30% PEG 4000 ...Details: A 2ul drop with 2 mg/ml protein, 5 mM Calcium chloride, 5mM Magnesium chloride, 2 mM ATP, 2mM Pyruvate, 1 mM EDTA, 200 mM Ammonium acetate, 100 mM Sodium acetate, 0.01 mM DTT, 30% PEG 4000 was added to 2 ul drop containing 2 M sodium aceate, 0.1 M Tris pH 8.2 30% PEG 4000. After a week a rod like crystal was removed and soaked in a solution with 30% glycerol 1mM EDTA, 100 mM sodium acetate 200mM ammonium acetate and 12% PEG 4000. The crystal was put into a loop and flash cooled in liquid notrogen

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.98 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Feb 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.11→50 Å / Num. obs: 77150 / % possible obs: 99.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 22.98 Å2 / Rmerge(I) obs: 0.25 / Net I/σ(I): 5.8
Reflection shellResolution: 2.11→2.19 Å

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Processing

Software
NameVersionClassification
d*TREKdata scaling
PHENIXdev_2398refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AYL

1ayl


Resolution: 2.3→47.087 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 20.29
RfactorNum. reflection% reflection
Rfree0.2092 2006 8.43 %
Rwork0.1485 --
obs0.1535 23809 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 72.67 Å2 / Biso mean: 24.5497 Å2 / Biso min: 10.95 Å2
Refinement stepCycle: final / Resolution: 2.3→47.087 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4104 0 39 300 4443
Biso mean--24.84 28.22 -
Num. residues----526
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084239
X-RAY DIFFRACTIONf_angle_d0.9635761
X-RAY DIFFRACTIONf_chiral_restr0.056632
X-RAY DIFFRACTIONf_plane_restr0.006745
X-RAY DIFFRACTIONf_dihedral_angle_d12.2192503
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.3-2.35750.2511490.15271531
2.3575-2.42130.26491340.15911552
2.4213-2.49250.22421450.15171559
2.4925-2.5730.24391500.16121548
2.573-2.66490.25351340.16231556
2.6649-2.77160.22611560.16381543
2.7716-2.89770.22271310.16191566
2.8977-3.05050.24811470.17271530
3.0505-3.24150.23281390.16581567
3.2415-3.49170.23561440.16571554
3.4917-3.8430.20111440.13981553
3.843-4.39870.16881490.12341569
4.3987-5.54050.15311400.12311579
5-5.54050.17321440.14091596

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