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- PDB-5hr5: Bovine Heart 6-Phosphofructo-2-Kinase/Fructose-2,6-Bisphosphatase... -

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Basic information

Entry
Database: PDB / ID: 5hr5
TitleBovine Heart 6-Phosphofructo-2-Kinase/Fructose-2,6-Bisphosphatase (PFKFB2)
Components6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 2
KeywordsHydrolase / Transferase / Bovine PFKFB2
Function / homology
Function and homology information


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 metabolic process / glycolytic process / ATP 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / 1,4-DIETHYLENE DIOXIDE / 6-O-phosphono-beta-D-fructofuranose / CITRATE ANION / 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 2
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsCrochet, R.B.
CitationJournal: Proteins / Year: 2017
Title: Crystal structure of heart 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase (PFKFB2) and the inhibitory influence of citrate on substrate binding.
Authors: Crochet, R.B. / Kim, J.D. / Lee, H. / Yim, Y.S. / Kim, S.G. / Neau, D. / Lee, Y.H.
History
DepositionJan 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9625
Polymers60,9971
Non-polymers9654
Water9,098505
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.116, 169.482, 85.254
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1163-

HOH

21A-1195-

HOH

31A-1205-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 2 / PFK/FBPase 2 / 6PF-2-K/Fru-2 / 6-P2ase heart-type isozyme


Mass: 60997.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Tissue: Heart / Gene: PFKFB2 / Plasmid: pET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3
References: UniProt: P26285, 6-phosphofructo-2-kinase, fructose-2,6-bisphosphate 2-phosphatase
#3: Sugar ChemComp-F6P / 6-O-phosphono-beta-D-fructofuranose / FRUCTOSE-6-PHOSPHATE / 6-O-phosphono-beta-D-fructose / 6-O-phosphono-D-fructose / 6-O-phosphono-fructose


Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
b-D-Fruf6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 508 molecules

#2: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2
#4: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 505 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1:1 mixture of protein sample to a mother liquor, pH 7.5 100mM HEPES, pH 7.0 0.5% tacsimate, 13-16% polyethylene glycol 3350, and 3% dioxane.

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: CAMD / Beamline: GCPCC / Wavelength: 1.381 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.381 Å / Relative weight: 1
ReflectionResolution: 1.82→46.54 Å / Num. obs: 52151 / % possible obs: 97.2 % / Redundancy: 10.9 % / Net I/σ(I): 2.62

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Processing

Software
NameVersionClassification
PHENIX(1.10pre_2100)refinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1K6M

1k6m


Resolution: 1.82→10 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1618 2642 5.06 %
Rwork0.1386 --
obs0.1398 49160 97.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.82→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3461 0 62 505 4028
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093596
X-RAY DIFFRACTIONf_angle_d1.0994874
X-RAY DIFFRACTIONf_dihedral_angle_d19.091364
X-RAY DIFFRACTIONf_chiral_restr0.079534
X-RAY DIFFRACTIONf_plane_restr0.007617
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8196-1.85270.17681040.17412061X-RAY DIFFRACTION78
1.8527-1.88830.21661250.15712260X-RAY DIFFRACTION86
1.8883-1.92690.1871120.14912398X-RAY DIFFRACTION91
1.9269-1.96880.16941280.14982554X-RAY DIFFRACTION95
1.9688-2.01460.16231320.13772589X-RAY DIFFRACTION98
2.0146-2.06490.19251640.13672625X-RAY DIFFRACTION100
2.0649-2.12080.16331560.1342657X-RAY DIFFRACTION100
2.1208-2.18320.1621500.12842659X-RAY DIFFRACTION100
2.1832-2.25360.15631380.12612643X-RAY DIFFRACTION100
2.2536-2.33420.16091580.12342648X-RAY DIFFRACTION100
2.3342-2.42760.15551460.12422688X-RAY DIFFRACTION100
2.4276-2.53810.16351300.13252682X-RAY DIFFRACTION100
2.5381-2.67190.16461420.132675X-RAY DIFFRACTION100
2.6719-2.83930.16551520.13992664X-RAY DIFFRACTION100
2.8393-3.05850.17541460.14152692X-RAY DIFFRACTION100
3.0585-3.36620.15131420.14322693X-RAY DIFFRACTION100
3.3662-3.85310.15021590.13632700X-RAY DIFFRACTION100
3.8531-4.85370.13331350.12392760X-RAY DIFFRACTION100
4.8537-100.18491230.16932876X-RAY DIFFRACTION100
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.32670.01540.11020.31490.29230.3054-0.00880.00930.06390.0275-0.0450.1649-0.1289-0.0871-0.00290.1265-0.0048-0.01050.1419-0.00610.148626.446246.003821.215
20.54630.2907-0.13480.74530.12290.7514-0.03350.0390.0039-0.0008-0.04280.19710.0711-0.1812-0.01520.1079-0.032-0.00950.186-0.02680.170616.049833.803720.5209
30.0115-0.02860.01910.0784-0.05090.06630.0852-0.4638-0.09010.2315-0.13380.1236-0.0463-0.00550.00430.2458-0.08550.0650.3189-0.01110.206119.11128.523240.2439
40.29070.0832-0.00770.4337-0.0080.2281-0.01760.0541-0.05020.0513-0.01510.03090.05270.003400.0904-0.00450.01350.1426-0.00610.123534.175237.711423.5628
50.7225-0.05530.19310.38790.44950.6129-0.0511-0.15770.01330.10940.0271-0.0449-0.11920.0527-0.01190.15230.0037-0.00830.1333-0.00680.127938.467869.78243.3581
60.48210.0314-0.06231.02010.13360.9816-0.00090.01680.0136-0.1036-0.03330.1186-0.1079-0.1171-0.01010.11020.018-0.00880.1017-0.01340.107329.568266.904131.0966
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 28 through 66 )
2X-RAY DIFFRACTION2chain 'A' and (resid 67 through 161 )
3X-RAY DIFFRACTION3chain 'A' and (resid 162 through 199 )
4X-RAY DIFFRACTION4chain 'A' and (resid 200 through 256 )
5X-RAY DIFFRACTION5chain 'A' and (resid 257 through 315 )
6X-RAY DIFFRACTION6chain 'A' and (resid 316 through 451 )

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