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- PDB-9e33: Polaromonas naphthalenivorans phosphoenolpyruvate carboxykinase i... -

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Basic information

Entry
Database: PDB / ID: 9.0E+33
TitlePolaromonas naphthalenivorans phosphoenolpyruvate carboxykinase in complex with PEP (C2221)
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
: / PHOSPHOENOLPYRUVATE / Phosphoenolpyruvate carboxykinase [GTP]
Similarity search - Component
Biological speciesPolaromonas naphthalenivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsMcLeod, M.J. / Barwell, S.A.E. / 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)68,5763
Polymers68,3531
Non-polymers2232
Water7,260403
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)74.501, 110.700, 162.816
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-1153-

HOH

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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-PEP / PHOSPHOENOLPYRUVATE


Mass: 168.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5O6P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / Source method: isolated from a natural source / Formula: H2O
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: 49.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
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 PEP. 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: 1.74→81.41 Å / Num. obs: 69062 / % possible obs: 100 % / Redundancy: 13 % / Biso Wilson estimate: 31.8 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.022 / Rrim(I) all: 0.078 / Net I/σ(I): 12.3
Reflection shellResolution: 1.74→1.8 Å / Redundancy: 12.9 % / Rmerge(I) obs: 1.672 / Mean I/σ(I) obs: 0.36 / Num. unique obs: 6839 / CC1/2: 0.652 / CC star: 0.888 / Rpim(I) all: 0.48 / Rrim(I) all: 1.741 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.74→81.41 Å / SU ML: 0.2432 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.4072
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2336 3446 4.99 %
Rwork0.202 65593 -
obs0.2036 69039 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.98 Å2
Refinement stepCycle: LAST / Resolution: 1.74→81.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4677 0 11 403 5091
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00394845
X-RAY DIFFRACTIONf_angle_d0.65156593
X-RAY DIFFRACTIONf_chiral_restr0.0448699
X-RAY DIFFRACTIONf_plane_restr0.0052857
X-RAY DIFFRACTIONf_dihedral_angle_d11.34471740
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.770.32631400.31622572X-RAY DIFFRACTION99.56
1.77-1.790.34921290.30052594X-RAY DIFFRACTION99.85
1.79-1.820.31671380.28652623X-RAY DIFFRACTION100
1.82-1.850.32881380.27642590X-RAY DIFFRACTION99.93
1.85-1.880.29971100.27862591X-RAY DIFFRACTION99.85
1.88-1.910.29751470.27932637X-RAY DIFFRACTION99.96
1.91-1.940.35981380.27082564X-RAY DIFFRACTION99.96
1.94-1.980.32271360.26682609X-RAY DIFFRACTION100
1.98-2.020.29371380.24612611X-RAY DIFFRACTION100
2.02-2.060.27391400.242588X-RAY DIFFRACTION99.96
2.06-2.110.27411430.22832608X-RAY DIFFRACTION100
2.11-2.170.28091340.22722605X-RAY DIFFRACTION99.96
2.17-2.220.2771470.2332623X-RAY DIFFRACTION100
2.22-2.290.2641250.2312609X-RAY DIFFRACTION99.96
2.29-2.360.24671550.2292587X-RAY DIFFRACTION99.96
2.36-2.450.26661440.22562602X-RAY DIFFRACTION100
2.45-2.550.27121440.22312623X-RAY DIFFRACTION100
2.55-2.660.25611330.22292659X-RAY DIFFRACTION100
2.66-2.80.24151650.21422560X-RAY DIFFRACTION100
2.8-2.980.23091240.2242663X-RAY DIFFRACTION100
2.98-3.210.28961410.21752645X-RAY DIFFRACTION100
3.21-3.530.23511170.19782666X-RAY DIFFRACTION100
3.53-4.040.16421390.1692662X-RAY DIFFRACTION100
4.04-5.090.19111200.15072709X-RAY DIFFRACTION100
5.09-81.410.18141610.16722793X-RAY DIFFRACTION99.76

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