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- PDB-9e37: Polaromonas naphthalenivorans phosphoenolpyruvate carboxykinase i... -

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Basic information

Entry
Database: PDB / ID: 9.0E+37
TitlePolaromonas naphthalenivorans phosphoenolpyruvate carboxykinase in complex with oxalate 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 / : / OXALATE ION / TRIETHYLENE GLYCOL / Phosphoenolpyruvate carboxykinase [GTP]
Similarity search - Component
Biological speciesPolaromonas naphthalenivorans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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)69,4327
Polymers68,3531
Non-polymers1,0796
Water9,170509
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)68.489, 85.557, 112.857
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, 515 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-OXL / OXALATE ION


Mass: 88.019 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2O4 / 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.: 509 / 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: 2.42 Å3/Da / Density % sol: 49.15 %
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 oxalate and 10 mM GTP. 15 mg/mL PnPEPCK

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jan 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→30.5 Å / Num. obs: 49489 / % possible obs: 98.9 % / Redundancy: 13.1 % / Biso Wilson estimate: 30.6 Å2 / CC1/2: 0.962 / CC star: 0.999 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.033 / Rrim(I) all: 0.124 / Net I/σ(I): 13.8
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.637 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 4114 / CC1/2: 0.824 / CC star: 0.95 / Rpim(I) all: 0.244 / Rrim(I) all: 0.686 / % possible all: 91.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
CRANKphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30.5 Å / SU ML: 0.2362 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.4407
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1983 2143 4.76 %
Rwork0.1635 42831 -
obs0.1652 44974 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.59 Å2
Refinement stepCycle: LAST / Resolution: 2→30.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4745 0 66 509 5320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00245009
X-RAY DIFFRACTIONf_angle_d0.59366827
X-RAY DIFFRACTIONf_chiral_restr0.0435723
X-RAY DIFFRACTIONf_plane_restr0.0047886
X-RAY DIFFRACTIONf_dihedral_angle_d13.97281809
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.35581380.26942499X-RAY DIFFRACTION88.02
2.05-2.10.24171460.21222786X-RAY DIFFRACTION97.99
2.1-2.160.24761260.1852853X-RAY DIFFRACTION99.47
2.16-2.220.2021420.17742840X-RAY DIFFRACTION99.77
2.22-2.290.24891470.18442821X-RAY DIFFRACTION99.7
2.29-2.370.21651340.16842879X-RAY DIFFRACTION99.7
2.37-2.470.19021120.16612854X-RAY DIFFRACTION99.7
2.47-2.580.23981630.18092851X-RAY DIFFRACTION99.9
2.58-2.720.23671280.18532880X-RAY DIFFRACTION99.83
2.72-2.890.23841330.18532891X-RAY DIFFRACTION99.87
2.89-3.110.2281540.1852866X-RAY DIFFRACTION99.9
3.11-3.420.20951510.17332919X-RAY DIFFRACTION99.93
3.42-3.910.16841450.14622897X-RAY DIFFRACTION99.87
3.91-4.930.14981590.12712937X-RAY DIFFRACTION99.87
4.93-30.50.16391650.1413058X-RAY DIFFRACTION99.97

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