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- PDB-1k6m: Crystal Structure of Human Liver 6-Phosphofructo-2-Kinase/Fructos... -

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Basic information

Entry
Database: PDB / ID: 1k6m
TitleCrystal Structure of Human Liver 6-Phosphofructo-2-Kinase/Fructose-2,6-Bisphosphatase
Components6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2-phosphatase
KeywordsTransferase / Hydrolase / tissue differentiation / isoform / domain stability
Function / homology
Function and homology information


positive regulation of glucokinase activity / 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase complex / 6-phosphofructo-2-kinase / 6-phosphofructo-2-kinase activity / fructose 2,6-bisphosphate metabolic process / fructose-2,6-bisphosphate 2-phosphatase / fructose-2,6-bisphosphate 2-phosphatase activity / fructose-6-phosphate binding / PKA-mediated phosphorylation of key metabolic factors / PP2A-mediated dephosphorylation of key metabolic factors ...positive regulation of glucokinase activity / 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase complex / 6-phosphofructo-2-kinase / 6-phosphofructo-2-kinase activity / fructose 2,6-bisphosphate metabolic process / fructose-2,6-bisphosphate 2-phosphatase / fructose-2,6-bisphosphate 2-phosphatase activity / fructose-6-phosphate binding / PKA-mediated phosphorylation of key metabolic factors / PP2A-mediated dephosphorylation of key metabolic factors / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / fructose metabolic process / negative regulation of glycolytic process / response to glucagon / response to starvation / animal organ regeneration / response to glucocorticoid / response to cAMP / positive regulation of glycolytic process / gluconeogenesis / glycolytic process / response to insulin / kinase binding / ATP binding / identical protein binding / cytosol
Similarity search - Function
Fructose-2,6-bisphosphatase / 6-phosphofructo-2-kinase / 6-phosphofructo-2-kinase / Phosphoglycerate/bisphosphoglycerate mutase, active site / Phosphoglycerate mutase family phosphohistidine signature. / Phosphoglycerate mutase family / Phosphoglycerate mutase-like / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Histidine phosphatase superfamily ...Fructose-2,6-bisphosphatase / 6-phosphofructo-2-kinase / 6-phosphofructo-2-kinase / Phosphoglycerate/bisphosphoglycerate mutase, active site / Phosphoglycerate mutase family phosphohistidine signature. / Phosphoglycerate mutase family / Phosphoglycerate mutase-like / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Histidine phosphatase superfamily / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / PHOSPHATE ION / 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLee, Y.H. / Li, Y. / Uyeda, K. / Hasemann, C.A.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Tissue-specific structure/function differentiation of the liver isoform of 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase.
Authors: Lee, Y.H. / Li, Y. / Uyeda, K. / Hasemann, C.A.
History
DepositionOct 16, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2012Group: Non-polymer description
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2-phosphatase
B: 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,8168
Polymers100,3902
Non-polymers1,4266
Water7,152397
1
A: 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2-phosphatase
hetero molecules

A: 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,8168
Polymers100,3902
Non-polymers1,4266
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
2
B: 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2-phosphatase
hetero molecules

B: 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,8168
Polymers100,3902
Non-polymers1,4266
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)74.980, 185.330, 89.670
Angle α, β, γ (deg.)90.00, 90.70, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-608-

HOH

21A-759-

HOH

31A-794-

HOH

41B-727-

HOH

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Components

#1: Protein 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2-phosphatase


Mass: 50195.035 Da / Num. of mol.: 2 / Mutation: W67F, W301F, W322F, D409E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET3c / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3
References: UniProt: P16118, 6-phosphofructo-2-kinase, fructose-2,6-bisphosphate 2-phosphatase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 397 / 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: 3.1 Å3/Da / Density % sol: 60.36 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: PEG 4000, Tris, sodium phosphate, , pH 8.0, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
pH: 7.25
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112 mg/mlprotein1drop
220 mMTris-HCl1droppH7.25
310 mMNaPi1drop
415 %glycerol1drop
50.5 mMEDTA1drop
610 mMdithiothreitol1drop
76 mMATP gammaS/Mg1dropor ADP
85-10 mMFru-6-P1drop
950 mMTris-HCl1reservoirpH7.5
1020-25 %ethylene glycol1reservoir
118 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 31, 1999 / Details: mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. all: 42142 / Num. obs: 42142 / % possible obs: 95.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Biso Wilson estimate: 51.8 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 20.1
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 94.4 % / Redundancy: 3.6 % / Mean I/σ(I) obs: 2

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
CNSrefinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1bif

1bif


Resolution: 2.4→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.257 4214 9.99 %Random
Rwork0.217 ---
all0.217 42142 --
obs0.217 42142 10 %-
Displacement parametersBiso mean: 41.1 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7054 0 82 397 7533
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_dihedral_angle_d29.6
X-RAY DIFFRACTIONx_angle_deg1.9
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg29.6

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