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- PDB-4gmu: Structure of rat cytosolic PEPCK Ld_1g in complex with oxalate and GTP -

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Basic information

Entry
Database: PDB / ID: 4gmu
TitleStructure of rat cytosolic PEPCK Ld_1g in complex with oxalate and GTP
ComponentsPhosphoenolpyruvate carboxykinase, cytosolic [GTP]
KeywordsLYASE / kinase / gluconeogenesis
Function / homology
Function and homology information


Gluconeogenesis / response to methionine / phosphoenolpyruvate carboxykinase activity / protein serine kinase activity (using GTP as donor) / positive regulation of transcription from RNA polymerase II promoter in response to acidic pH / cellular response to potassium ion starvation / cellular response to fructose stimulus / glycerol biosynthetic process from pyruvate / Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases / phosphoenolpyruvate carboxykinase (GTP) ...Gluconeogenesis / response to methionine / phosphoenolpyruvate carboxykinase activity / protein serine kinase activity (using GTP as donor) / positive regulation of transcription from RNA polymerase II promoter in response to acidic pH / cellular response to potassium ion starvation / cellular response to fructose stimulus / glycerol biosynthetic process from pyruvate / Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases / phosphoenolpyruvate carboxykinase (GTP) / phosphoenolpyruvate carboxykinase (GTP) activity / propionate catabolic process / regulation of lipid biosynthetic process / response to interleukin-6 / oxaloacetate metabolic process / carboxylic acid binding / positive regulation of memory T cell differentiation / hepatocyte differentiation / cellular response to glucagon stimulus / nucleoside diphosphate kinase activity / response to starvation / response to lipid / cellular response to interleukin-1 / cellular response to dexamethasone stimulus / cellular response to retinoic acid / gluconeogenesis / cellular response to cAMP / response to activity / response to bacterium / response to insulin / cellular response to glucose stimulus / lipid metabolic process / 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 / cytosol / cytoplasm
Similarity search - Function
Phosphoenolpyruvate carboxykinase N-terminal domain / Phosphoenolpyruvate carboxykinase (GTP) signature. / Phosphoenolpyruvate carboxykinase C-terminal P-loop domain / 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; domain 3 - #20 / Phosphoenolpyruvate Carboxykinase; domain 2 / Phosphoenolpyruvate Carboxykinase, domain 2 ...Phosphoenolpyruvate carboxykinase N-terminal domain / Phosphoenolpyruvate carboxykinase (GTP) signature. / Phosphoenolpyruvate carboxykinase C-terminal P-loop domain / 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; domain 3 - #20 / Phosphoenolpyruvate Carboxykinase; domain 2 / Phosphoenolpyruvate Carboxykinase, domain 2 / Phosphoenolpyruvate Carboxykinase; domain 1 / Phosphoenolpyruvate Carboxykinase, domain 1 / 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
GUANOSINE-5'-TRIPHOSPHATE / : / OXALATE ION / Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2 Å
AuthorsJohnson, T.A. / Holyoak, T.
CitationJournal: Biochemistry / Year: 2012
Title: The {Omega}-loop lid domain of phosphoenolpyruvate carboxykinase is essential for catalytic function.
Authors: Johnson, T.A. / Holyoak, T.
History
DepositionAug 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name

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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)69,2887
Polymers68,4891
Non-polymers7996
Water15,853880
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.546, 85.521, 118.755
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 68489.484 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Pck1 / Plasmid: pSUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P07379, phosphoenolpyruvate carboxykinase (GTP)

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Non-polymers , 5 types, 886 molecules

#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Chemical ChemComp-MN / MANGANESE (II) ION


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-OXL / OXALATE ION / Oxalate


Mass: 88.019 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 880 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsRESIDUES 464-474 (ATAAAEHKGKV) OF PEPCK HAVE BEEN DELETED AND REPLACED BY A G LINKER.

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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: 2.24 Å3/Da / Density % sol: 45.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 22-26% PEG3350, 0.1 M HEPES, pH 7.4, 10 mM manganese chloride, 10 mM GTP, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 2, 2011
Details: Flat mirror (vertical focusing), single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal, asymmetric cut 4.965 degrees
Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.2→100 Å / Num. obs: 188021 / % possible obs: 97.9 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.04 / Χ2: 1.014 / Net I/σ(I): 18.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.2-1.243.20.349178400.993194
1.24-1.293.90.288189981.015199.6
1.29-1.353.90.219189360.993199.7
1.35-1.4240.165190260.99199.8
1.42-1.5140.112190860.982199.8
1.51-1.6340.075190541.008199.7
1.63-1.7940.055190860.991199.5
1.79-2.0540.042190511.023199.1
2.05-2.5940.04189261.06197.7
2.59-1004.10.022180181.082190.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DT2
Resolution: 1.2→26.97 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.961 / WRfactor Rfree: 0.2118 / WRfactor Rwork: 0.1838 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8814 / SU B: 0.602 / SU ML: 0.028 / SU R Cruickshank DPI: 0.0413 / SU Rfree: 0.0442 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.041 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1958 9440 5 %RANDOM
Rwork0.1702 ---
obs0.1715 187552 97.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 66.16 Å2 / Biso mean: 16.2133 Å2 / Biso min: 5.78 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.2→26.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4798 0 42 880 5720
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.025284
X-RAY DIFFRACTIONr_angle_refined_deg2.0561.9737217
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7945683
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.66424.146246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.38415932
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6821535
X-RAY DIFFRACTIONr_chiral_restr0.1190.2754
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0214102
LS refinement shellResolution: 1.2→1.232 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 650 -
Rwork0.255 11768 -
all-12418 -
obs--91.31 %

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