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- PDB-2rke: The Structure of rat cytosolic PEPCK in complex with sulfoacetate. -

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Basic information

Entry
Database: PDB / ID: 2rke
TitleThe Structure of rat cytosolic PEPCK in complex with sulfoacetate.
ComponentsPhosphoenolpyruvate carboxykinase, cytosolic [GTP]
KeywordsLYASE / kinase / gluconeogenesis / Decarboxylase / GTP-binding / Nucleotide-binding
Function / homology
Function and homology information


Gluconeogenesis / phosphoenolpyruvate carboxykinase activity / cellular response to potassium ion starvation / positive regulation of transcription from RNA polymerase II promoter in response to acidic pH / 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 / propionate catabolic process / cellular response to fructose stimulus ...Gluconeogenesis / phosphoenolpyruvate carboxykinase activity / cellular response to potassium ion starvation / positive regulation of transcription from RNA polymerase II promoter in response to acidic pH / 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 / propionate catabolic process / cellular response to fructose stimulus / phosphoenolpyruvate carboxykinase (GTP) activity / phosphoenolpyruvate carboxykinase (GTP) / regulation of lipid biosynthetic process / response to interleukin-6 / carboxylic acid binding / oxaloacetate metabolic process / hepatocyte differentiation / positive regulation of memory T cell 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 / response to activity / cellular response to cAMP / 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-utilising / Phosphoenolpyruvate carboxykinase, C-terminal P-loop domain / Phosphoenolpyruvate carboxykinase, GTP-utilising, conserved site / Phosphoenolpyruvate carboxykinase, GTP-utilising, N-terminal / Phosphoenolpyruvate carboxykinase C-terminal P-loop domain / Phosphoenolpyruvate carboxykinase (GTP) signature. / Phosphoenolpyruvate Carboxykinase; domain 3 - #20 / Phosphoenolpyruvate Carboxykinase, domain 1 / Phosphoenolpyruvate Carboxykinase; domain 1 ...Phosphoenolpyruvate carboxykinase N-terminal domain / Phosphoenolpyruvate carboxykinase, GTP-utilising / Phosphoenolpyruvate carboxykinase, C-terminal P-loop domain / Phosphoenolpyruvate carboxykinase, GTP-utilising, conserved site / Phosphoenolpyruvate carboxykinase, GTP-utilising, N-terminal / Phosphoenolpyruvate carboxykinase C-terminal P-loop domain / Phosphoenolpyruvate carboxykinase (GTP) signature. / Phosphoenolpyruvate Carboxykinase; domain 3 - #20 / Phosphoenolpyruvate Carboxykinase, domain 1 / Phosphoenolpyruvate Carboxykinase; domain 1 / Phosphoenolpyruvate Carboxykinase, domain 2 / 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
: / sulfoacetic acid / Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsSullivan, S.M. / Stiffin, R.M. / Carlson, G.M. / Holyoak, T.
CitationJournal: Biochemistry / Year: 2008
Title: Differential Inhibition of Cytosolic PEPCK by Substrate Analogues. Kinetic and Structural Characterization of Inhibitor Recognition.
Authors: Stiffin, R.M. / Sullivan, S.M. / Carlson, G.M. / Holyoak, T.
History
DepositionOct 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software

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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)70,0136
Polymers69,6441
Non-polymers3695
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)45.180, 119.031, 60.885
Angle α, β, γ (deg.)90.00, 108.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Phosphoenolpyruvate carboxykinase, cytosolic [GTP] / / Phosphoenolpyruvate carboxylase / 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 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P07379, phosphoenolpyruvate carboxykinase (GTP)

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Non-polymers , 5 types, 436 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-SAT / sulfoacetic acid


Mass: 140.115 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O5S
#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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 12-30% PEG 3350, 0.1M HEPES, 10 MM MNCL2, pH 7.4, temperature 298K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 8, 2007 / Details: BLUE OSMIC Confocal MIRRORS
RadiationMonochromator: Blue osmic mirrors / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→100 Å / Num. obs: 53184 / % possible obs: 94.7 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.094 / Χ2: 1.041 / Net I/σ(I): 13.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.863.70.52239091.042170.2
1.86-1.945.70.47247181.002184.3
1.94-2.0370.37452610.938193.7
2.03-2.1380.29855361.022199.1
2.13-2.279.10.23756291.1261100
2.27-2.449.50.18555761.0211100
2.44-2.699.80.14556141.0091100
2.69-3.089.80.10856171.0911100
3.08-3.889.90.07556291.0931100
3.88-1009.90.05356951.011199.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3data extraction
CrystalCleardata collection
RefinementResolution: 1.8→29.09 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.938 / SU B: 7.3 / SU ML: 0.118 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.163 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.249 2687 5.1 %RANDOM
Rwork0.203 ---
obs0.205 53125 94.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.011 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0.05 Å2
2---0.02 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4812 0 16 431 5259
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225077
X-RAY DIFFRACTIONr_angle_refined_deg1.2371.9666900
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9145649
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.44624.31232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.01115891
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5631531
X-RAY DIFFRACTIONr_chiral_restr0.0870.2722
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023915
X-RAY DIFFRACTIONr_nbd_refined0.190.22422
X-RAY DIFFRACTIONr_nbtor_refined0.3030.23401
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2404
X-RAY DIFFRACTIONr_metal_ion_refined0.1020.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.231
X-RAY DIFFRACTIONr_mcbond_it0.5181.53105
X-RAY DIFFRACTIONr_mcangle_it0.90325019
X-RAY DIFFRACTIONr_scbond_it1.37832066
X-RAY DIFFRACTIONr_scangle_it2.1884.51861
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 140 -
Rwork0.347 2549 -
all-2689 -
obs--64.94 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.7156-0.4383-0.4023.7167-0.18210.56930.0520.17680.0178-0.55770.0619-0.0584-0.0577-0.0978-0.11390.0936-0.0175-0.00620.0840.0048-0.0208-0.2489-15.8254-21.8126
20.66980.2434-0.39021.4315-0.05061.42360.01130.0397-0.11340.226-0.02710.08360.24120.00140.01580.060.0027-0.0127-0.02830.00550.0339-1.9113-21.43182.3472
30.35610.01310.40013.37711.11620.80880.06820.0894-0.0184-0.10360.0732-0.4098-0.12770.0415-0.1414-0.0512-0.0306-0.01610.0969-0.02510.072515.10173.4848-4.2389
40.21940.16480.09821.24130.38030.1280.03070.07150.05160.0956-0.07310.09130.0547-0.00180.0424-0.02780.0111-0.04560.08150.010.0490.6473-8.3006-4.7095
51.5595-0.1434-1.03130.0615-0.1451.8735-0.19430.0554-0.19840.1271-0.01340.06950.1253-0.01920.20770.0765-0.02560.06510.0028-0.01920.0876-13.69465.265913.4121
60.5446-0.93550.26712.4855-0.07260.301-0.03660.0834-0.0520.6304-0.08630.41540.1409-0.03660.1230.2338-0.06940.1318-0.0202-0.00080.0134-8.0711-11.468616.8522
70.0326-0.1467-0.11790.65980.53040.4264-0.11540.01370.02640.23610.02420.05160.11260.0240.09120.09820.00560.02330.0480.02380.0323-1.92173.923713.663
82.25440.25480.27950.5208-0.2860.6855-0.1067-0.2189-0.05610.0786-0.07420.11140.0393-0.02660.18090.05630.02930.0160.05060.015-0.0013-10.340514.999323.1742
90.48920.20.98540.27441.23595.58790.4841-1.43560.2786-0.217-0.11990.21960.0164-0.2681-0.36410.09840.02310.07320.19240.16880.2072-10.707312.438935.3171
100.7906-0.8537-0.57880.96280.38831.7854-0.1027-0.03160.07050.12180.1042-0.0996-0.10410.1549-0.00160.0303-0.0167-0.06240.04870.00420.03967.852323.999117.1232
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 366 - 38
2X-RAY DIFFRACTION2AA37 - 8939 - 91
3X-RAY DIFFRACTION3AA90 - 13492 - 136
4X-RAY DIFFRACTION4AA135 - 258137 - 260
5X-RAY DIFFRACTION5AA259 - 317261 - 319
6X-RAY DIFFRACTION6AA318 - 385320 - 387
7X-RAY DIFFRACTION7AA386 - 500388 - 502
8X-RAY DIFFRACTION8AA501 - 562503 - 564
9X-RAY DIFFRACTION9AA563 - 579565 - 581
10X-RAY DIFFRACTION10AA580 - 622582 - 624

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