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- PDB-9e36: Polaromonas naphthalenivorans phosphoenolpyruvate carboxykinase i... -

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Basic information

Entry
Database: PDB / ID: 9.0E+36
TitlePolaromonas naphthalenivorans phosphoenolpyruvate carboxykinase in complex with beta-sulfopyruvate and GTP
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
GUANOSINE-5'-TRIPHOSPHATE / : / TRIETHYLENE GLYCOL / SULFOPYRUVATE / Phosphoenolpyruvate carboxykinase [GTP]
Similarity search - Component
Biological speciesPolaromonas naphthalenivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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)69,5127
Polymers68,3531
Non-polymers1,1596
Water13,061725
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)68.523, 85.607, 113.799
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 , 7 types, 731 molecules

#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 725 / 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: 2.44 Å3/Da / Density % sol: 49.62 %
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, 10 mM beta-sulfopyruvate and 10 mM GTP. 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: 1.1271 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: 1.1271 Å / Relative weight: 1
ReflectionResolution: 1.8→53.5 Å / Num. obs: 62447 / % possible obs: 99.8 % / Redundancy: 13 % / Biso Wilson estimate: 16.31 Å2 / CC1/2: 0.989 / CC star: 0.997 / Rmerge(I) obs: 0.277 / Rpim(I) all: 0.079 / Rrim(I) all: 0.288 / Net I/σ(I): 4.6
Reflection shellResolution: 1.8→1.87 Å / Redundancy: 13.3 % / Rmerge(I) obs: 1.949 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 6058 / CC1/2: 0.757 / CC star: 0.928 / Rpim(I) all: 0.546 / Rrim(I) all: 2.025 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→53.5 Å / SU ML: 0.2078 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.0273
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1917 3114 4.99 %
Rwork0.1595 59294 -
obs0.161 62408 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.58 Å2
Refinement stepCycle: LAST / Resolution: 1.8→53.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4745 0 70 725 5540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00685097
X-RAY DIFFRACTIONf_angle_d0.88556955
X-RAY DIFFRACTIONf_chiral_restr0.0546733
X-RAY DIFFRACTIONf_plane_restr0.0083905
X-RAY DIFFRACTIONf_dihedral_angle_d14.91661857
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.830.30271310.2692556X-RAY DIFFRACTION95.69
1.83-1.860.29111770.25232637X-RAY DIFFRACTION99.72
1.86-1.890.2691620.22132594X-RAY DIFFRACTION99.86
1.89-1.930.22421390.20552697X-RAY DIFFRACTION99.86
1.93-1.960.24911260.20012663X-RAY DIFFRACTION99.96
1.96-20.23111400.18792668X-RAY DIFFRACTION99.86
2-2.050.21491300.17992688X-RAY DIFFRACTION100
2.05-2.090.20911460.16892660X-RAY DIFFRACTION100
2.09-2.150.23231250.17222724X-RAY DIFFRACTION99.96
2.15-2.210.19541460.17092639X-RAY DIFFRACTION100
2.21-2.270.19481390.17192690X-RAY DIFFRACTION100
2.27-2.340.21631420.17152674X-RAY DIFFRACTION100
2.34-2.430.18951290.15672710X-RAY DIFFRACTION100
2.43-2.520.21661490.15312683X-RAY DIFFRACTION100
2.52-2.640.18261300.15042716X-RAY DIFFRACTION100
2.64-2.780.19631450.14872695X-RAY DIFFRACTION100
2.78-2.950.19581400.16192705X-RAY DIFFRACTION99.96
2.95-3.180.1851470.1562713X-RAY DIFFRACTION100
3.18-3.50.17471500.14652720X-RAY DIFFRACTION100
3.5-4.010.14571370.1272753X-RAY DIFFRACTION100
4.01-5.050.13551250.12182810X-RAY DIFFRACTION100
5.05-53.50.16041590.15042899X-RAY DIFFRACTION100

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