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- PDB-7l3m: PEPCK MMQX structure 40ms post-mixing with oxaloacetic acid -

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Basic information

Entry
Database: PDB / ID: 7l3m
TitlePEPCK MMQX structure 40ms post-mixing with oxaloacetic acid
ComponentsPhosphoenolpyruvate carboxykinase, cytosolic [GTP]
KeywordsLYASE / PEPCK / phosphoenolpyruvate carboxykinase / gluconeogensis
Function / homology
Function and homology information


Gluconeogenesis / phosphoenolpyruvate carboxykinase activity / cellular response to potassium ion starvation / protein serine kinase activity (using GTP as donor) / response to methionine / glycerol biosynthetic process from pyruvate / Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases / phosphoenolpyruvate carboxykinase (GTP) / phosphoenolpyruvate carboxykinase (GTP) activity / propionate catabolic process ...Gluconeogenesis / phosphoenolpyruvate carboxykinase activity / cellular response to potassium ion starvation / protein serine kinase activity (using GTP as donor) / response to methionine / glycerol biosynthetic process from pyruvate / Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases / phosphoenolpyruvate carboxykinase (GTP) / phosphoenolpyruvate carboxykinase (GTP) activity / propionate catabolic process / cellular response to raffinose / tricarboxylic acid metabolic process / regulation of lipid biosynthetic process / response to interleukin-6 / cellular response to fructose stimulus / cellular hypotonic response / glyceraldehyde-3-phosphate biosynthetic process / carboxylic acid binding / cellular hypotonic salinity response / cellular response to phorbol 13-acetate 12-myristate / oxaloacetate metabolic process / hepatocyte differentiation / cellular hyperosmotic response / positive regulation of memory T cell differentiation / nucleoside diphosphate kinase activity / cellular hyperosmotic salinity response / response to lipid / response to starvation / cellular response to glucagon stimulus / cellular response to interleukin-1 / positive regulation of lipid biosynthetic process / cellular response to retinoic acid / cellular response to cAMP / cellular response to dexamethasone stimulus / response to nutrient levels / response to activity / gluconeogenesis / cellular response to glucose stimulus / response to bacterium / response to insulin / lipid metabolic process / cellular response to insulin stimulus / glucose metabolic process / GDP binding / glucose homeostasis / manganese ion binding / cellular response to tumor necrosis factor / cellular response to hypoxia / peptidyl-serine phosphorylation / response to lipopolysaccharide / GTP binding / magnesium ion binding / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / cytosol / cytoplasm
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
CARBON DIOXIDE / GUANOSINE-5'-DIPHOSPHATE / : / PHOSPHOENOLPYRUVATE / Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.07 Å
AuthorsClinger, J.A. / Moreau, D.W. / McLeod, M.J. / Holyoak, T. / Thorne, R.E.
Funding support United States, Canada, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM127528-01 United States
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Iucrj / Year: 2021
Title: Millisecond mix-and-quench crystallography (MMQX) enables time-resolved studies of PEPCK with remote data collection.
Authors: Clinger, J.A. / Moreau, D.W. / McLeod, M.J. / Holyoak, T. / Thorne, R.E.
History
DepositionDec 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,4878
Polymers69,6441
Non-polymers8437
Water5,747319
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.389, 118.935, 60.300
Angle α, β, γ (deg.)90.000, 109.421, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Phosphoenolpyruvate carboxykinase, cytosolic [GTP] / / PEPCK-C


Mass: 69643.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Pck1 / Plasmid: PGEX4T2 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P07379, phosphoenolpyruvate carboxykinase (GTP), Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases

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Non-polymers , 6 types, 326 molecules

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


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PEP / PHOSPHOENOLPYRUVATE / Phosphoenolpyruvic acid


Mass: 168.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5O6P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#6: Chemical ChemComp-CO2 / CARBON DIOXIDE / Carbon dioxide


Mass: 44.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 319 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.16 Å3/Da / Density % sol: 43.03 % / Mosaicity: 0 °
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5 / Details: 25mM MnCl2, 25mM GTP, 19% PEG 3350, 100mM HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 1.12 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 2.07→59.47 Å / Num. obs: 35893 / % possible obs: 99.9 % / Redundancy: 3.6 % / CC1/2: 0.967 / Rmerge(I) obs: 0.168 / Rpim(I) all: 0.103 / Rrim(I) all: 0.198 / Net I/σ(I): 6.1 / Num. measured all: 127837 / Scaling rejects: 1078
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.07-2.123.31.011887826660.4280.6471.2072.199.8
9.26-59.473.50.05714974240.9860.0340.06711.899.7

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Processing

Software
NameVersionClassification
PHENIX1.19.2refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
DIALS1.14.5data reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6P5O

6p5o


Resolution: 2.07→51.33 Å / SU ML: 0.239 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.6799
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.186 1857 5.18 %
Rwork0.1722 33981 -
obs0.1729 35838 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.64 Å2
Refinement stepCycle: LAST / Resolution: 2.07→51.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4791 0 45 319 5155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00695043
X-RAY DIFFRACTIONf_angle_d0.94796849
X-RAY DIFFRACTIONf_chiral_restr0.0519718
X-RAY DIFFRACTIONf_plane_restr0.0059892
X-RAY DIFFRACTIONf_dihedral_angle_d16.1481898
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.130.32451550.27232538X-RAY DIFFRACTION97.29
2.13-2.190.25581400.24682598X-RAY DIFFRACTION99.53
2.19-2.260.27391270.22582615X-RAY DIFFRACTION99.64
2.26-2.340.23991320.20292631X-RAY DIFFRACTION99.75
2.34-2.430.18881570.18692577X-RAY DIFFRACTION99.6
2.43-2.540.21931270.18142614X-RAY DIFFRACTION99.82
2.54-2.680.19671840.17242589X-RAY DIFFRACTION99.89
2.68-2.850.19121480.17412616X-RAY DIFFRACTION99.96
2.85-3.070.18151480.16812611X-RAY DIFFRACTION99.96
3.07-3.370.16071430.16162632X-RAY DIFFRACTION99.89
3.37-3.860.14941130.14082645X-RAY DIFFRACTION99.96
3.86-4.860.12961490.13452633X-RAY DIFFRACTION100
4.87-51.330.16621340.15632682X-RAY DIFFRACTION99.89
Refinement TLS params.Method: refined / Origin x: -2.16834553195 Å / Origin y: -0.234906753778 Å / Origin z: 7.74140547381 Å
111213212223313233
T0.122548683341 Å2-0.0124544592705 Å20.0248280667006 Å2-0.0926463601824 Å20.0128591700687 Å2--0.117472943894 Å2
L0.32657562098 °2-0.0302376695049 °2-0.0290115001479 °2-0.619451416862 °20.213732296774 °2--0.469361568119 °2
S-0.00402161689087 Å °0.028282215442 Å °-0.0512248955928 Å °0.0614014436621 Å °-0.0314855412015 Å °-0.00926876191227 Å °0.0362161881993 Å °0.000998523352667 Å °0.0176081826799 Å °
Refinement TLS groupSelection details: all

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