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- PDB-3dt4: The structure of rat cytosolic PEPCK in complex with oxalate and GTP -

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Basic information

Entry
Database: PDB / ID: 3dt4
TitleThe structure of rat cytosolic PEPCK in complex with oxalate and GTP
ComponentsPhosphoenolpyruvate carboxykinase, cytosolic [GTP]
KeywordsLYASE / kinase / gluconeogenesis / Decarboxylase / GTP-binding / Nucleotide-binding
Function / homology
Function and homology information


Gluconeogenesis / phosphoenolpyruvate carboxykinase activity / protein serine kinase activity (using GTP as donor) / cellular response to potassium ion starvation / positive regulation of transcription from RNA polymerase II promoter in response to acidic pH / 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 / protein serine kinase activity (using GTP as donor) / cellular response to potassium ion starvation / positive regulation of transcription from RNA polymerase II promoter in response to acidic pH / 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, GTP-utilising / Phosphoenolpyruvate carboxykinase, GTP-utilising, conserved site / Phosphoenolpyruvate carboxykinase, C-terminal P-loop domain / Phosphoenolpyruvate carboxykinase (GTP) signature. / Phosphoenolpyruvate carboxykinase, GTP-utilising, N-terminal / Phosphoenolpyruvate carboxykinase N-terminal domain / Phosphoenolpyruvate carboxykinase C-terminal P-loop domain / Phosphoenolpyruvate Carboxykinase; domain 2 / Phosphoenolpyruvate Carboxykinase, domain 2 / 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, GTP-utilising, N-terminal / Phosphoenolpyruvate carboxykinase N-terminal domain / Phosphoenolpyruvate carboxykinase C-terminal P-loop domain / Phosphoenolpyruvate Carboxykinase; domain 2 / Phosphoenolpyruvate Carboxykinase, domain 2 / Phosphoenolpyruvate Carboxykinase; domain 1 / Phosphoenolpyruvate Carboxykinase, domain 1 / Phosphoenolpyruvate Carboxykinase; domain 3 - #20 / 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 / Resolution: 1.45 Å
AuthorsSullivan, S.M. / Holyoak, T.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Enzymes with lid-gated active sites must operate by an induced fit mechanism instead of conformational selection.
Authors: Sullivan, S.M. / Holyoak, T.
History
DepositionJul 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 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]
C: Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,01413
Polymers139,2882
Non-polymers1,72611
Water26,4641469
1
A: Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6267
Polymers69,6441
Non-polymers9826
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3886
Polymers69,6441
Non-polymers7445
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.454, 119.759, 87.300
Angle α, β, γ (deg.)90.000, 96.700, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AC

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


Mass: 69643.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Pck1 / Plasmid: PGEX4T2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P07379, phosphoenolpyruvate carboxykinase (GTP)

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Non-polymers , 6 types, 1480 molecules

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


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


Mass: 88.019 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2O4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1469 / 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: 2.25 Å3/Da / Density % sol: 45.41 %
Crystal growTemperature: 298 K / Method: hanging drop vapor diffusion / pH: 7.4
Details: 12-30% PEG 3350, 0.1M HEPES, 10 MM MNCL2, pH 7.4, hanging drop vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 4, 2007
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 degs
Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.45→100 Å / Num. obs: 217132 / % possible obs: 99.8 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.08 / Χ2: 1.077 / Net I/σ(I): 9.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.45-1.55.70.717212891.039198
1.5-1.566.70.567216871.0891100
1.56-1.636.90.433217191.0961100
1.63-1.7270.337216971.1171100
1.72-1.837.10.237217541.1081100
1.83-1.977.20.165217081.1191100
1.97-2.177.40.117217701.0821100
2.17-2.487.60.085217571.0421100
2.48-3.127.80.0632182711100
3.12-1007.70.045219241.078199.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
Blu-Iceicedata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 1.45→30.02 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.85 / SU B: 2.644 / SU ML: 0.046 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.203 10901 5 %RANDOM
Rwork0.175 ---
obs0.176 217074 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 52.02 Å2 / Biso mean: 11.462 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å2-0.03 Å2
2---0.04 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.45→30.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9731 0 92 1469 11292
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02210303
X-RAY DIFFRACTIONr_angle_refined_deg1.6011.96914006
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.03851300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.06624.246464
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.63151775
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4861561
X-RAY DIFFRACTIONr_chiral_restr0.1110.21464
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0217921
X-RAY DIFFRACTIONr_mcbond_it0.9151.56278
X-RAY DIFFRACTIONr_mcangle_it1.538210141
X-RAY DIFFRACTIONr_scbond_it2.47134025
X-RAY DIFFRACTIONr_scangle_it3.9184.53837
LS refinement shellResolution: 1.45→1.487 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 721 -
Rwork0.296 14744 -
all-15465 -
obs--97.14 %
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)
11.2222-1.0219-0.22951.66910.33070.97530.14710.08570.0821-0.1543-0.0782-0.30690.04430.0995-0.0690.06950.03490.04720.0411-0.00070.058141.197-17.90635.488
20.9993-0.24560.43580.3343-0.0690.61440.08670.0283-0.18040.02980.02840.03870.15950.05-0.1150.07660.00380.00360.0528-0.00430.032521.183-14.48946.062
30.6112-0.40040.05871.1140.29690.55610.05650.02520.0053-0.0289-0.0225-0.12430.04140.0489-0.0340.08350.00890.03080.0870.00780.039731.734-7.87244.174
40.4346-0.20850.13020.6813-0.20380.53140.03260.0487-0.0671-0.07420.0030.05130.0377-0.0087-0.03560.0911-0.00310.01140.0785-0.00350.028813.646-3.16439.7
50.456-0.16490.06060.60250.01270.46710.0009-0.03450.0114-0.00230.01740.0441-0.0268-0.066-0.01840.0675-0.0010.01970.08030.00920.02067.51411.35746.905
61.1327-0.812-0.05230.899-0.04850.25060.0830.157-0.122-0.1909-0.084-0.08960.05910.10430.0010.09930.02510.02430.0666-0.02130.053932.253-15.32479.53
70.5041-0.33910.09690.72-0.14310.3026-0.0027-0.0336-0.01280.0220.0048-0.04860.04440.0351-0.00210.07040.00020.01340.0852-0.00080.031123.122-1.36192.488
80.934-0.357-0.04351.26860.35671.22860.05330.0536-0.0924-0.0651-0.0458-0.01830.04580.085-0.00750.11110.01230.02830.0935-0.01040.054324.949-7.64782.534
90.5864-0.09330.13570.5714-0.13860.5340.02130.0364-0.0773-0.06910.01460.06090.0301-0.0085-0.0360.0821-0.00280.00450.0701-0.00780.03058.6711.22282.88
100.5838-0.08210.18620.5623-0.04910.5544-0.0238-0.06410.03210.01280.02140.046-0.0433-0.08680.00240.06770.00920.01180.0795-0.00210.02812.05515.46490.022
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 536 - 55
2X-RAY DIFFRACTION2AA54 - 10156 - 103
3X-RAY DIFFRACTION3AA102 - 209104 - 211
4X-RAY DIFFRACTION4AA210 - 386212 - 388
5X-RAY DIFFRACTION5AA387 - 622389 - 624
6X-RAY DIFFRACTION6CB3 - 675 - 69
7X-RAY DIFFRACTION7CB68 - 15170 - 153
8X-RAY DIFFRACTION8CB152 - 209154 - 211
9X-RAY DIFFRACTION9CB210 - 386212 - 388
10X-RAY DIFFRACTION10CB387 - 622389 - 624

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