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- PDB-1bif: 6-PHOSPHOFRUCTO-2-KINASE/FRUCTOSE-2,6-BISPHOSPHATASE BIFUNCTIONAL... -

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Basic information

Entry
Database: PDB / ID: 1bif
Title6-PHOSPHOFRUCTO-2-KINASE/FRUCTOSE-2,6-BISPHOSPHATASE BIFUNCTIONAL ENZYME COMPLEXED WITH ATP-G-S AND PHOSPHATE
Components6-PHOSPHOFRUCTO-2-KINASE/ FRUCTOSE-2,6-BISPHOSPHATASE
KeywordsBIFUNCTIONAL ENZYME / KINASE / TRANSFERASE (PHOSPHO) / PHOSPHATASE / HYDROLASE (PHOSPHO) / GLYCOLYSIS
Function / homology
Function and homology information


Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / 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 / 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 / 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 4
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2 Å
AuthorsHasemann, C.A. / Deisenhofer, J.
CitationJournal: Structure / Year: 1996
Title: The crystal structure of the bifunctional enzyme 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase reveals distinct domain homologies.
Authors: Hasemann, C.A. / Istvan, E.S. / Uyeda, K. / Deisenhofer, J.
History
DepositionNov 8, 1996Processing site: BNL
Revision 1.0Nov 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 15, 2012Group: Non-polymer description
Revision 1.4Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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_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

Downloads & links

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Assembly

Deposited unit
A: 6-PHOSPHOFRUCTO-2-KINASE/ FRUCTOSE-2,6-BISPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8986
Polymers54,0691
Non-polymers8305
Water5,747319
1
A: 6-PHOSPHOFRUCTO-2-KINASE/ FRUCTOSE-2,6-BISPHOSPHATASE
hetero molecules

A: 6-PHOSPHOFRUCTO-2-KINASE/ FRUCTOSE-2,6-BISPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,79612
Polymers108,1372
Non-polymers1,65910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Unit cell
Length a, b, c (Å)83.000, 83.000, 130.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 6-PHOSPHOFRUCTO-2-KINASE/ FRUCTOSE-2,6-BISPHOSPHATASE


Mass: 54068.582 Da / Num. of mol.: 1 / Mutation: W15F, W64F, W299F, W320F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell line: BL21 / Gene: RT2K / Organ: TESTISTesticle / Plasmid: PT7-7 / Cell line (production host): BL21 / Gene (production host): RT2K / Production host: Escherichia coli (E. coli)
References: UniProt: P25114, 6-phosphofructo-2-kinase, fructose-2,6-bisphosphate 2-phosphatase

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Non-polymers , 5 types, 324 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: 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.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 319 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE N-TERMINAL 36 AMINO ACIDS OF THE PROTEIN WERE NOT VISIBLE IN THE ELECTRON DENSITY. PROTEIN ...THE N-TERMINAL 36 AMINO ACIDS OF THE PROTEIN WERE NOT VISIBLE IN THE ELECTRON DENSITY. PROTEIN SEQUENCE ANALYSIS OF A REDISSOLVED CRYSTAL CONFIRMED THE PRESENCE OF THE N-TERMINUS IN THE CRYSTALS. THE CONCLUSION IS THEN THAT THE N-TERMINAL 36 AMINO ACIDS ARE DISORDERED.

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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: 2.41 Å3/Da / Density % sol: 48.9 %
Crystal growpH: 6
Details: PROTEIN WAS CRYSTALLISED FROM 50MM SUCCINATE, PH 6.0, 10MM HEPES PH 7.0, 18% PEG 4000, 1% N-OCTYLGLUCOSIDE
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
250 mMTris-PO41drop
35 %glycerol1drop
40.5 mMEDTA1drop
51 %PEG4001drop
610 mMDTT1drop
73 mM1dropMgCl2
81 mMATP gamma S1drop
91 mMF6P1drop
1115 %PEG40001reservoir
1250 mMsuccinate1reservoir
1310 mMHEPES1reservoir
142 %n-octylglucosude1reservoir
10reservoir solution1drop

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Mar 15, 1995 / Details: YALE MIRRORS
RadiationMonochromator: YALE MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 29479 / % possible obs: 90 % / Observed criterion σ(I): -3 / Redundancy: 2 % / Biso Wilson estimate: 23.6 Å2 / Rsym value: 0.032 / Net I/σ(I): 21.6
Reflection shellResolution: 2→2.05 Å / Redundancy: 1.56 % / Mean I/σ(I) obs: 3.7 / Rsym value: 0.281 / % possible all: 60.6
Reflection
*PLUS
Lowest resolution: 20 Å / Rmerge(I) obs: 0.032

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 2→6 Å / Rfactor Rfree error: 0.0046 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0 / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.25 2918 10 %RANDOM
Rwork0.183 ---
obs0.183 29479 85.6 %-
Displacement parametersBiso mean: 31.8 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å / Luzzati d res low obs: 4 Å / Luzzati sigma a obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3506 0 48 319 3873
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.55
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.43
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2→2.09 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.302 197 10 %
Rwork0.276 2155 -
obs--55.35 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1ENGH & HUBERENGH & HUBER
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.43

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