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- PDB-9e32: Holo Polaromonas naphthalenivorans phosphoenolpyruvate carboxykinase -

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Basic information

Entry
Database: PDB / ID: 9.0E+32
TitleHolo Polaromonas naphthalenivorans phosphoenolpyruvate carboxykinase
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
: / DI(HYDROXYETHYL)ETHER / Phosphoenolpyruvate carboxykinase [GTP]
Similarity search - Component
Biological speciesPolaromonas naphthalenivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 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)68,5143
Polymers68,3531
Non-polymers1612
Water9,242513
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)68.185, 73.396, 112.788
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

#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 / Plasmid: pESUMOstar (KAN) / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A1VIE9, phosphoenolpyruvate carboxykinase (GTP)
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 513 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.06 Å3/Da / Density % sol: 40.42 %
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 and 30-40% PEG 8000. 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: 1.53→61.52 Å / Num. obs: 86593 / % possible obs: 93.4 % / Redundancy: 11.9 % / Biso Wilson estimate: 22.4 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.042 / Rrim(I) all: 0.145 / Net I/σ(I): 8.03
Reflection shellResolution: 1.53→1.59 Å / Redundancy: 12.3 % / Rmerge(I) obs: 1.593 / Mean I/σ(I) obs: 0.29 / Num. unique obs: 8427 / CC1/2: 0.823 / CC star: 0.95 / Rpim(I) all: 0.465 / Rrim(I) all: 1.661 / % possible all: 61.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.53→61.52 Å / SU ML: 0.2643 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.979
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.229 3831 4.73 %
Rwork0.1945 77200 -
obs0.1961 81031 93.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.66 Å2
Refinement stepCycle: LAST / Resolution: 1.53→61.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4687 0 8 513 5208
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00424887
X-RAY DIFFRACTIONf_angle_d0.69666654
X-RAY DIFFRACTIONf_chiral_restr0.0472706
X-RAY DIFFRACTIONf_plane_restr0.0055868
X-RAY DIFFRACTIONf_dihedral_angle_d12.14171759
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.540.5018700.42251647X-RAY DIFFRACTION54.11
1.54-1.570.3572960.39911980X-RAY DIFFRACTION65.22
1.57-1.590.40391090.37872068X-RAY DIFFRACTION68.52
1.59-1.610.3641050.37542290X-RAY DIFFRACTION75.72
1.61-1.630.37011180.362500X-RAY DIFFRACTION82.66
1.63-1.660.39161530.35052600X-RAY DIFFRACTION86.22
1.66-1.690.36821370.33142749X-RAY DIFFRACTION92
1.69-1.720.31441300.31322974X-RAY DIFFRACTION97.03
1.72-1.750.33091500.29693023X-RAY DIFFRACTION99.47
1.75-1.780.31531540.28433032X-RAY DIFFRACTION100
1.78-1.820.31311660.26312994X-RAY DIFFRACTION99.97
1.82-1.860.2981760.25323027X-RAY DIFFRACTION100
1.86-1.90.28151520.23533041X-RAY DIFFRACTION100
1.9-1.950.28161520.23983030X-RAY DIFFRACTION100
1.95-20.27881680.24113018X-RAY DIFFRACTION100
2-2.060.25121760.2073035X-RAY DIFFRACTION100
2.06-2.120.23961370.18583078X-RAY DIFFRACTION100
2.12-2.20.23111340.18083041X-RAY DIFFRACTION100
2.2-2.290.2271380.19313096X-RAY DIFFRACTION99.97
2.29-2.390.23581530.18843047X-RAY DIFFRACTION100
2.39-2.520.23381460.19053079X-RAY DIFFRACTION99.97
2.52-2.680.24411520.18963063X-RAY DIFFRACTION99.97
2.68-2.880.25211470.18623097X-RAY DIFFRACTION100
2.88-3.170.22151370.17973119X-RAY DIFFRACTION100
3.17-3.630.17711350.16033128X-RAY DIFFRACTION99.94
3.63-4.580.14871740.13893160X-RAY DIFFRACTION100
4.58-61.520.1871660.15613284X-RAY DIFFRACTION99.94

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