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- PDB-1khb: PEPCK complex with nonhydrolyzable GTP analog, native data -

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Basic information

Entry
Database: PDB / ID: 1khb
TitlePEPCK complex with nonhydrolyzable GTP analog, native data
ComponentsPhosphoenolpyruvate carboxykinase, cytosolic (GTP)
KeywordsLYASE / Gluconeogenesis / P-loop
Function / homology
Function and homology information


positive regulation of transcription from RNA polymerase II promoter in response to acidic pH / protein serine kinase activity (using GTP as donor) / cellular response to potassium ion starvation / Abacavir metabolism / response to methionine / glycerol biosynthetic process from pyruvate / Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases / propionate catabolic process / cellular response to fructose stimulus / phosphoenolpyruvate carboxykinase (GTP) ...positive regulation of transcription from RNA polymerase II promoter in response to acidic pH / protein serine kinase activity (using GTP as donor) / cellular response to potassium ion starvation / Abacavir metabolism / response to methionine / glycerol biosynthetic process from pyruvate / Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases / propionate catabolic process / cellular response to fructose stimulus / phosphoenolpyruvate carboxykinase (GTP) / phosphoenolpyruvate carboxykinase (GTP) activity / regulation of lipid biosynthetic process / response to interleukin-6 / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / carboxylic acid binding / oxaloacetate metabolic process / hepatocyte differentiation / positive regulation of memory T cell differentiation / Gluconeogenesis / cellular response to glucagon stimulus / response to starvation / response to lipid / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / cellular response to interleukin-1 / cellular response to dexamethasone stimulus / cellular response to retinoic acid / gluconeogenesis / response to activity / cellular response to cAMP / response to insulin / cellular response to glucose stimulus / Transcriptional regulation of white adipocyte differentiation / GDP binding / cellular response to insulin stimulus / glucose metabolic process / glucose homeostasis / cellular response to tumor necrosis factor / cellular response to hypoxia / manganese ion binding / response to lipopolysaccharide / aging / peptidyl-serine phosphorylation / GTP binding / magnesium ion binding / endoplasmic reticulum / mitochondrion / extracellular exosome / 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) signature. / Phosphoenolpyruvate carboxykinase C-terminal P-loop domain / Phosphoenolpyruvate carboxykinase, GTP-utilising, N-terminal / Phosphoenolpyruvate carboxykinase N-terminal domain / Phosphoenolpyruvate Carboxykinase, domain 2 / Phosphoenolpyruvate Carboxykinase; domain 3 - #20 / Phosphoenolpyruvate Carboxykinase, domain 1 ...Phosphoenolpyruvate carboxykinase, GTP-utilising / Phosphoenolpyruvate carboxykinase, GTP-utilising, conserved site / Phosphoenolpyruvate carboxykinase, C-terminal P-loop domain / Phosphoenolpyruvate carboxykinase (GTP) signature. / Phosphoenolpyruvate carboxykinase C-terminal P-loop domain / Phosphoenolpyruvate carboxykinase, GTP-utilising, N-terminal / Phosphoenolpyruvate carboxykinase N-terminal domain / Phosphoenolpyruvate Carboxykinase, domain 2 / Phosphoenolpyruvate Carboxykinase; domain 3 - #20 / Phosphoenolpyruvate Carboxykinase, domain 1 / Phosphoenolpyruvate Carboxykinase; domain 1 / Phosphoenolpyruvate Carboxykinase; domain 2 / Phosphoenolpyruvate carboxykinase, C-terminal / Phosphoenolpyruvate carboxykinase, N-terminal / Phosphoenolpyruvate Carboxykinase; domain 3 / Beta Complex / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / : / Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.854 Å
AuthorsDunten, P. / Belunis, C. / Crowther, R. / Hollfelder, K. / Kammlott, U. / Levin, W. / Michel, H. / Ramsey, G.B. / Swain, A. / Weber, D. / Wertheimer, S.J.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Crystal structure of human cytosolic phosphoenolpyruvate carboxykinase reveals a new GTP-binding site.
Authors: Dunten, P. / Belunis, C. / Crowther, R. / Hollfelder, K. / Kammlott, U. / Levin, W. / Michel, H. / Ramsey, G.B. / Swain, A. / Weber, D. / Wertheimer, S.J.
History
DepositionNov 29, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoenolpyruvate carboxykinase, cytosolic (GTP)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3447
Polymers69,5301
Non-polymers8146
Water4,179232
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.400, 60.580, 62.000
Angle α, β, γ (deg.)88.40, 70.30, 72.63
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Phosphoenolpyruvate carboxykinase, cytosolic (GTP) / / Phosphoenolpyruvate carboxylase / PEPCK / PEPCK-C


Mass: 69529.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCK1 / Production host: Escherichia coli (E. coli)
References: UniProt: P35558, phosphoenolpyruvate carboxykinase (GTP)

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Non-polymers , 5 types, 238 molecules

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


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Comment: GMP-PCP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O

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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: 2.2 Å3/Da / Density % sol: 43.96 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG1500, MES, DTT, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11
25 mg/mlprotein1drop
330 mMHEPES-KOH1droppH7.5
42.5 mM1dropMgCl2
51 mMspermidine1drop
630 %(v/v)MPD1reservoir
70.1 Msodium citrate1reservoirpH5.6
80.2 Mammonium acetate1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.072 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 1.854→20 Å / Num. obs: 47525 / % possible obs: 94.7 % / Rsym value: 0.027
Reflection
*PLUS
Rmerge(I) obs: 0.027

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Processing

Software
NameClassification
REFMACrefinement
MAR345data collection
SCALEPACKdata scaling
RefinementResolution: 1.854→20 Å / SU B: 1.69009 / SU ML: 0.05201 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15395 / ESU R Free: 0.14197
RfactorNum. reflection% reflectionSelection details
Rfree0.22473 2383 5 %RANDOM
Rwork0.18188 ---
obs0.184 47525 94.7 %-
Displacement parametersBiso mean: 14.902 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20.07 Å20.02 Å2
2--0.32 Å2-0.53 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.854→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4721 0 46 232 4999
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0220.021
X-RAY DIFFRACTIONp_mcbond_it1.1761.5
X-RAY DIFFRACTIONp_mcangle_it1.9372
X-RAY DIFFRACTIONp_scbond_it3.1433
X-RAY DIFFRACTIONp_scangle_it4.8014.5
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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