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- PDB-9e35: Polaromonas naphthalenivorans phosphoenolpyruvate carboxykinase i... -

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Basic information

Entry
Database: PDB / ID: 9.0E+35
TitlePolaromonas naphthalenivorans phosphoenolpyruvate carboxykinase in complex with beta-sulfopyruvate
ComponentsPhosphoenolpyruvate carboxykinase [GTP]
KeywordsLYASE / Inhibitor complex / Metabolic enzyme / Multi-temperature / Ambient temperature
Function / homology
Function and homology information


phosphoenolpyruvate carboxykinase (GTP) / phosphoenolpyruvate carboxykinase (GTP) activity / glycerol biosynthetic process from pyruvate / propionate catabolic process / oxaloacetate metabolic process / response to starvation / response to lipid / gluconeogenesis / cellular response to glucose stimulus / kinase activity ...phosphoenolpyruvate carboxykinase (GTP) / phosphoenolpyruvate carboxykinase (GTP) activity / glycerol biosynthetic process from pyruvate / propionate catabolic process / oxaloacetate metabolic process / response to starvation / response to lipid / gluconeogenesis / cellular response to glucose stimulus / kinase activity / manganese ion binding / GTP binding / cytosol
Similarity search - Function
Phosphoenolpyruvate carboxykinase, GTP-utilising / Phosphoenolpyruvate carboxykinase, GTP-utilising, conserved site / Phosphoenolpyruvate carboxykinase, C-terminal P-loop domain / Phosphoenolpyruvate carboxykinase, GTP-utilising, N-terminal / Phosphoenolpyruvate carboxykinase C-terminal P-loop domain / Phosphoenolpyruvate carboxykinase N-terminal domain / Phosphoenolpyruvate carboxykinase (GTP) signature. / Phosphoenolpyruvate carboxykinase, C-terminal / Phosphoenolpyruvate carboxykinase, N-terminal
Similarity search - Domain/homology
: / TRIETHYLENE GLYCOL / SULFOPYRUVATE / Phosphoenolpyruvate carboxykinase [GTP]
Similarity search - Component
Biological speciesPolaromonas naphthalenivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsMcLeod, M.J. / Holyoak, T.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Protein Sci. / Year: 2025
Title: Structural mechanisms for cold-adapted activity of phosphoenolpyruvate carboxykinase.
Authors: McLeod, M.J. / Yazdani, S. / Barwell, S.A.E. / Holyoak, T.
History
DepositionOct 23, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoenolpyruvate carboxykinase [GTP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9215
Polymers68,3531
Non-polymers5674
Water8,431468
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.784, 86.097, 113.423
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Phosphoenolpyruvate carboxykinase [GTP] / PEP carboxykinase / PEPCK / GTP-dependent phosphoenolpyruvate carboxykinase / GTP-PEPCK


Mass: 68353.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Polaromonas naphthalenivorans (bacteria)
Gene: pckG, Pnap_0102, Pck1 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A1VIE9, phosphoenolpyruvate carboxykinase (GTP)

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Non-polymers , 5 types, 472 molecules

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


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-SPV / SULFOPYRUVATE


Mass: 168.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O6S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 468 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.46 Å3/Da / Density % sol: 49.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100 mM TRIS-Cl pH 8.0, 0.4 M LiCl2, 5 mM MgCl2, 1 mM MnCl2, 30-40% PEG 8000 and 10 mM beta-sulfopyruvate. 15 mg/mL PnPEPCK

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: 7B2 / Wavelength: 0.9686 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jan 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.71→68.6 Å / Num. obs: 72872 / % possible obs: 96.1 % / Redundancy: 12.6 % / Biso Wilson estimate: 27.58 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.05 / Rrim(I) all: 0.179 / Net I/σ(I): 5.7
Reflection shellResolution: 1.71→1.77 Å / Redundancy: 12.6 % / Rmerge(I) obs: 2.74 / Mean I/σ(I) obs: 0.26 / Num. unique obs: 6932 / CC1/2: 0.655 / CC star: 0.89 / Rpim(I) all: 0.805 / Rrim(I) all: 2.855 / % possible all: 73.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.71→68.58 Å / SU ML: 0.3237 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.7215
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2292 3464 4.93 %
Rwork0.189 66867 -
obs0.191 70331 96.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.78 Å2
Refinement stepCycle: LAST / Resolution: 1.71→68.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4745 0 34 468 5247
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00674988
X-RAY DIFFRACTIONf_angle_d0.79946793
X-RAY DIFFRACTIONf_chiral_restr0.0511721
X-RAY DIFFRACTIONf_plane_restr0.0065886
X-RAY DIFFRACTIONf_dihedral_angle_d12.36421800
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.740.4562810.43521707X-RAY DIFFRACTION61.98
1.74-1.760.41751200.40382188X-RAY DIFFRACTION79.56
1.76-1.790.38141220.39882388X-RAY DIFFRACTION87.61
1.79-1.810.39191290.39442444X-RAY DIFFRACTION88.45
1.81-1.840.44261350.39342492X-RAY DIFFRACTION90.68
1.84-1.880.421390.37512587X-RAY DIFFRACTION94.75
1.88-1.910.3641480.31332777X-RAY DIFFRACTION99.76
1.91-1.950.33971260.27912723X-RAY DIFFRACTION99.72
1.95-1.990.28461420.25172751X-RAY DIFFRACTION99.86
1.99-2.030.24711610.22782753X-RAY DIFFRACTION100
2.03-2.080.24791170.2192782X-RAY DIFFRACTION99.86
2.08-2.130.28251290.21872761X-RAY DIFFRACTION99.97
2.13-2.190.24181450.21542740X-RAY DIFFRACTION99.86
2.19-2.250.27011400.20922805X-RAY DIFFRACTION100
2.25-2.320.23411480.20342770X-RAY DIFFRACTION100
2.32-2.410.23361220.18292777X-RAY DIFFRACTION100
2.41-2.50.26281510.17942787X-RAY DIFFRACTION100
2.5-2.620.23861490.1872766X-RAY DIFFRACTION100
2.62-2.760.25621640.18382783X-RAY DIFFRACTION100
2.76-2.930.20881320.18832784X-RAY DIFFRACTION100
2.93-3.150.20451540.18162814X-RAY DIFFRACTION100
3.15-3.470.21811550.16612792X-RAY DIFFRACTION100
3.47-3.970.18451520.14472831X-RAY DIFFRACTION100
3.97-5.010.16461490.12792859X-RAY DIFFRACTION99.97
5.01-68.580.17091540.14633006X-RAY DIFFRACTION99.91

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