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- PDB-2qew: Rat cytosolic PEPCK, in complex with manganese ion. -

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Basic information

Entry
Database: PDB / ID: 2qew
TitleRat cytosolic PEPCK, in complex with manganese ion.
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 ...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 fructose stimulus / cellular response to raffinose / tricarboxylic acid metabolic process / regulation of lipid biosynthetic process / response to interleukin-6 / cellular hypotonic response / cellular hypotonic salinity response / carboxylic acid binding / glyceraldehyde-3-phosphate biosynthetic process / 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 / response to bacterium / cellular response to glucose stimulus / response to insulin / lipid metabolic process / cellular response to insulin stimulus / GDP binding / glucose metabolic process / glucose homeostasis / manganese ion binding / cellular response to tumor necrosis factor / cellular response to hypoxia / peptidyl-serine phosphorylation / response to lipopolysaccharide / GTP binding / magnesium ion binding / endoplasmic reticulum / 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; 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-utilising, N-terminal / Phosphoenolpyruvate carboxykinase C-terminal P-loop domain / Phosphoenolpyruvate carboxykinase N-terminal domain / Phosphoenolpyruvate carboxykinase (GTP) signature. / 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
: / Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSullivan, S.M. / Holyoak, T.
CitationJournal: Biochemistry / Year: 2007
Title: Structures of rat cytosolic PEPCK: insight into the mechanism of phosphorylation and decarboxylation of oxaloacetic acid.
Authors: Sullivan, S.M. / Holyoak, T.
History
DepositionJun 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Jan 24, 2018Group: Structure summary / Category: entity_name_com / Item: _entity_name_com.name
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)69,7774
Polymers69,6441
Non-polymers1333
Water10,431579
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.448, 119.046, 60.599
Angle α, β, γ (deg.)90.00, 109.59, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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)
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 579 / 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: 2.17 Å3/Da / Density % sol: 43.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 12-30% PEG 3350, 0.1M HEPES pH 7.4, 10 mM MnCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 28, 2007 / Details: Blue osmic confocal
RadiationMonochromator: Blue osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 53469 / Num. obs: 53469 / % possible obs: 97.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.3 % / Rmerge(I) obs: 0.08 / Χ2: 1.045 / Net I/σ(I): 13.1
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.546 / Num. unique all: 5077 / Χ2: 0.979 / % possible all: 93.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KHG
Resolution: 1.8→24.26 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.936 / SU ML: 0.083 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.213 2721 5.1 %RANDOM
Rwork0.178 ---
all0.18 53450 --
obs0.18 53450 97.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.668 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20.05 Å2
2---0.15 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.8→24.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4819 0 3 579 5401
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224982
X-RAY DIFFRACTIONr_angle_refined_deg1.0791.9626752
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4665621
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.12424.196224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.58515859
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5041530
X-RAY DIFFRACTIONr_chiral_restr0.0750.2709
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023822
X-RAY DIFFRACTIONr_nbd_refined0.1820.22426
X-RAY DIFFRACTIONr_nbtor_refined0.3020.23375
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.110.2498
X-RAY DIFFRACTIONr_metal_ion_refined0.1110.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.281
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1270.238
X-RAY DIFFRACTIONr_mcbond_it0.3951.53067
X-RAY DIFFRACTIONr_mcangle_it0.73124942
X-RAY DIFFRACTIONr_scbond_it1.10632009
X-RAY DIFFRACTIONr_scangle_it1.8474.51805
LS refinement shellResolution: 1.8→1.849 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 195 -
Rwork0.301 3442 -
obs-3637 90.45 %
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)
11.1203-0.3469-1.14141.9320.6781.2232-0.02170.2036-0.0037-0.21560.0663-0.0164-0.0823-0.0762-0.04460.0232-0.0202-0.03210.07860.0077-0.00131.049-16.76-20.306
21.13080.0191-0.39650.7476-0.54211.44810.0925-0.0676-0.1030.1050.0140.0240.2488-0.0124-0.10640.00650.0087-0.0259-0.0068-0.01980.0144-1.854-19.4494.752
33.96562.88851.99852.93861.85762.6449-0.29120.0795-0.2101-0.28410.2578-0.4721-0.19330.05890.0334-0.0063-0.01360.0486-0.0013-0.03030.086615.02611.552-0.066
40.9399-0.1086-0.42420.76880.3770.4390.05870.02460.0636-0.0480.0351-0.0374-0.00460.0097-0.0938-0.0091-0.0032-0.01320.0415-0.01270.03582.867-10.436-6.093
50.3205-0.89660.05393.17290.16390.15820.04960.04290.0124-0.0576-0.03030.021-0.0320.021-0.0192-0.0265-0.01340.0080.082-0.01940.0571.621-0.023-3.032
62.729-0.1549-0.79590.15980.00690.7733-0.0176-0.134-0.19750.01280.0137-0.0076-0.0488-0.00640.0038-0.00030.0010.00680.03520.01790.0685-14.2057.75413.59
70.9671.1435-0.58241.3537-0.60754.77520.0088-0.4572-0.4030.04190.0652-0.28910.02390.1722-0.07390.00620.00630.01070.01160.06690.1121-13.0131.13821.729
82.3665-0.4337-1.03611.61010.51240.5216-0.00240.0774-0.0483-0.1543-0.04150.02960.1182-0.01420.0439-0.0383-0.0026-0.01050.0350.0030.0531-14.7147.2246.109
90.9428-0.52720.68571.26160.05391.7540.0061-0.0535-0.02180.24240.02130.16910.06140.0122-0.02740.0368-0.02940.00740.02610.00660.0138-7.058-13.96917.655
108.48750.2957-6.20164.2803-0.10348.9957-0.1482-0.7867-0.60480.6568-0.0005-0.25710.44450.69910.14870.10670.0413-0.10630.01960.0673-0.08251.554-23.16924.915
110.6215-0.53480.17151.2850.15020.1549-0.0073-0.0082-0.00460.1367-0.03850.1050.01090.01520.04590.0138-0.01190.02040.07460.02370.0266-10.39-2.67111.339
121.1550.1559-0.13380.26060.250.6974-0.0551-0.0744-0.128-0.00820.0335-0.0464-0.0180.00320.02160.015-0.0072-0.01330.02370.01980.04492.10213.73913.339
131.88230.5295-0.33250.5008-0.23550.5988-0.0074-0.2621-0.15560.0354-0.06310.053-0.00280.00530.0704-0.00660.0101-0.01160.06350.02760.0154-9.32912.66621.865
141.69770.3208-0.2760.63560.00481.0206-0.0004-0.28470.04240.1085-0.0678-0.0496-0.07990.01660.06820.0080.0121-0.02980.0452-0.0015-0.0029-0.3220.05923.471
151.21620.43030.68352.33841.815912.78170.0587-0.04680.01680.09150.0206-0.2968-0.13820.276-0.0793-0.0007-0.0011-0.05430.00710.01760.06524.63628.99618.46
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 445 - 46
2X-RAY DIFFRACTION2AA45 - 9447 - 96
3X-RAY DIFFRACTION3AA95 - 11697 - 118
4X-RAY DIFFRACTION4AA117 - 224119 - 226
5X-RAY DIFFRACTION5AA225 - 260227 - 262
6X-RAY DIFFRACTION6AA261 - 286263 - 288
7X-RAY DIFFRACTION7AA287 - 302289 - 304
8X-RAY DIFFRACTION8AA303 - 328305 - 330
9X-RAY DIFFRACTION9AA329 - 373331 - 375
10X-RAY DIFFRACTION10AA374 - 392376 - 394
11X-RAY DIFFRACTION11AA397 - 435399 - 437
12X-RAY DIFFRACTION12AA436 - 499438 - 501
13X-RAY DIFFRACTION13AA500 - 546502 - 548
14X-RAY DIFFRACTION14AA547 - 607549 - 609
15X-RAY DIFFRACTION15AA608 - 622610 - 624

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