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- PDB-7l3v: PEPCK MMQX structure 120ms post-mixing with oxaloacetic acid -

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Basic information

Entry
Database: PDB / ID: 7l3v
TitlePEPCK MMQX structure 120ms post-mixing with oxaloacetic acid
ComponentsPhosphoenolpyruvate carboxykinase, cytosolic [GTP]
KeywordsLYASE / PEPCK / phosphoenolpyruvate carboxykinase / gluconeogenesis
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 hypotonic response / cellular response to fructose stimulus / cellular hypotonic salinity response / glyceraldehyde-3-phosphate biosynthetic process / carboxylic acid binding / 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 / positive regulation of lipid biosynthetic process / cellular response to interleukin-1 / 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 / GDP binding / glucose metabolic process / glucose homeostasis / cellular response to tumor necrosis factor / manganese ion binding / 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: 1.98 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:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)70,5198
Polymers69,6441
Non-polymers8757
Water7,764431
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.159, 118.787, 61.307
Angle α, β, γ (deg.)90.000, 107.246, 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 , 5 types, 438 molecules

#2: Chemical ChemComp-CO2 / CARBON DIOXIDE / Carbon dioxide


Mass: 44.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO2
#3: 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
#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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 431 / 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: 2.3 Å3/Da / Density % sol: 46.51 % / 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: 1.98→44.08 Å / Num. obs: 43818 / % possible obs: 99.9 % / Redundancy: 3.6 % / CC1/2: 0.939 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.093 / Rrim(I) all: 0.176 / Net I/σ(I): 5.4 / Num. measured all: 156224 / Scaling rejects: 1207
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
1.98-2.033.51.2581115832320.5080.8161.5061.499.7
8.85-44.083.60.07618505100.9840.0450.08911.799.5

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Processing

Software
NameVersionClassification
PHENIX1.19.2refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
DIALSdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 7L36

7l36


Resolution: 1.98→41.67 Å / SU ML: 0.2291 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.4082
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2063 2198 5.03 %
Rwork0.1864 41517 -
obs0.1874 43715 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.41 Å2
Refinement stepCycle: LAST / Resolution: 1.98→41.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4684 0 45 431 5160
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01074924
X-RAY DIFFRACTIONf_angle_d1.18516687
X-RAY DIFFRACTIONf_chiral_restr0.0608704
X-RAY DIFFRACTIONf_plane_restr0.0072871
X-RAY DIFFRACTIONf_dihedral_angle_d16.99521846
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.020.32071540.28412444X-RAY DIFFRACTION94.23
2.02-2.070.29641410.27592522X-RAY DIFFRACTION98.92
2.07-2.120.31891330.2612634X-RAY DIFFRACTION99.57
2.12-2.180.30011300.24012566X-RAY DIFFRACTION99.59
2.18-2.240.37271190.26522631X-RAY DIFFRACTION99.67
2.24-2.310.31291150.25392625X-RAY DIFFRACTION99.42
2.31-2.390.21471320.20012577X-RAY DIFFRACTION99.82
2.39-2.490.21031490.18482585X-RAY DIFFRACTION99.74
2.49-2.60.20571450.18762613X-RAY DIFFRACTION99.93
2.6-2.740.20731490.18752578X-RAY DIFFRACTION99.89
2.74-2.910.19721290.18482631X-RAY DIFFRACTION99.86
2.91-3.140.19871620.1782575X-RAY DIFFRACTION99.93
3.14-3.450.17891420.16352616X-RAY DIFFRACTION99.96
3.45-3.950.15381200.15112630X-RAY DIFFRACTION99.93
3.95-4.980.15081250.13932641X-RAY DIFFRACTION99.93
4.98-41.670.18121530.17872649X-RAY DIFFRACTION99.96
Refinement TLS params.Method: refined / Origin x: -1.89243935544 Å / Origin y: -0.0284977261361 Å / Origin z: 8.13155691194 Å
111213212223313233
T0.306521350029 Å2-0.0469970881265 Å20.133897271025 Å2-0.214068888303 Å20.00511826739839 Å2--0.241000963652 Å2
L0.380769460389 °20.12382355535 °20.232654758317 °2-3.08258978197 °21.47283275991 °2--1.05215411173 °2
S0.0254386416641 Å °-0.0515394028873 Å °-0.0248544390712 Å °0.685850232607 Å °-0.201866450886 Å °0.422373789495 Å °0.373626657759 Å °-0.116210025507 Å °0.0481886115865 Å °
Refinement TLS groupSelection details: all

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