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- PDB-6pfk: PHOSPHOFRUCTOKINASE, INHIBITED T-STATE -

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Basic information

Entry
Database: PDB / ID: 6pfk
TitlePHOSPHOFRUCTOKINASE, INHIBITED T-STATE
ComponentsPHOSPHOFRUCTOKINASE
KeywordsTRANSFERASE / KINASE / GLYCOLYSIS
Function / homology
Function and homology information


6-phosphofructokinase complex / 6-phosphofructokinase / 6-phosphofructokinase activity / fructose-6-phosphate binding / fructose 1,6-bisphosphate metabolic process / fructose 6-phosphate metabolic process / monosaccharide binding / canonical glycolysis / AMP binding / ATP binding ...6-phosphofructokinase complex / 6-phosphofructokinase / 6-phosphofructokinase activity / fructose-6-phosphate binding / fructose 1,6-bisphosphate metabolic process / fructose 6-phosphate metabolic process / monosaccharide binding / canonical glycolysis / AMP binding / ATP binding / metal ion binding / identical protein binding
Similarity search - Function
ATP-dependent 6-phosphofructokinase, prokaryotic-type / ATP-dependent 6-phosphofructokinase, prokaryotic / Phosphofructokinase domain / Phosphofructokinase, conserved site / Phosphofructokinase signature. / Phosphofructokinase domain / ATP-dependent 6-phosphofructokinase / Phosphofructokinase superfamily / Phosphofructokinase / Rossmann fold - #450 ...ATP-dependent 6-phosphofructokinase, prokaryotic-type / ATP-dependent 6-phosphofructokinase, prokaryotic / Phosphofructokinase domain / Phosphofructokinase, conserved site / Phosphofructokinase signature. / Phosphofructokinase domain / ATP-dependent 6-phosphofructokinase / Phosphofructokinase superfamily / Phosphofructokinase / Rossmann fold - #450 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-PHOSPHOGLYCOLIC ACID / ATP-dependent 6-phosphofructokinase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsEvans, P.R. / Schirmer, T. / Auer, M.
CitationJournal: Nature / Year: 1990
Title: Structural basis of the allosteric behaviour of phosphofructokinase.
Authors: Schirmer, T. / Evans, P.R.
History
DepositionJan 4, 1996Processing site: BNL
SupersessionJul 11, 1996ID: 5PFK
Revision 1.0Jul 11, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 10, 2011Group: Other
Revision 1.4Mar 13, 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_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_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: PHOSPHOFRUCTOKINASE
B: PHOSPHOFRUCTOKINASE
C: PHOSPHOFRUCTOKINASE
D: PHOSPHOFRUCTOKINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,2968
Polymers136,6714
Non-polymers6244
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15870 Å2
ΔGint-65 kcal/mol
Surface area39060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.000, 115.200, 96.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.755319, -0.145439, -0.639016), (-0.142733, -0.988165, 0.056194), (-0.639626, 0.048764, -0.767138)34.97301, 27.50033, 89.84422
2given(-0.981476, 0.191581, 0.000946), (0.191514, 0.980978, 0.031679), (0.005141, 0.031273, -0.999498)27.80794, -4.2062, 90.71854
3given(-0.770518, -0.023227, 0.636995), (-0.044803, -0.994891, -0.090472), (0.635842, -0.09825, 0.76554)-1.29301, 32.81303, 2.33948

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Components

#1: Protein
PHOSPHOFRUCTOKINASE


Mass: 34167.852 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: INHIBITED T-STATE
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: PFK / Plasmid: DERIVATIVE OF PBR322 / Gene (production host): PFK / Production host: Escherichia coli (E. coli) / References: UniProt: P00512, 6-phosphofructokinase
#2: Chemical
ChemComp-PGA / 2-PHOSPHOGLYCOLIC ACID


Mass: 156.031 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C2H5O6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsNON-CRYSTALLOGRAPHIC SYMMETRY WAS RE-IMPOSED BY REPLICATING SUBUNIT D (THE BEST DEFINED), THEN ...NON-CRYSTALLOGRAPHIC SYMMETRY WAS RE-IMPOSED BY REPLICATING SUBUNIT D (THE BEST DEFINED), THEN REFINED WITH TIGHT NCS RESTRAINTS. NCS RESTRAINTS WERE THEN REMOVED, AND A SMALL NUMBER OF SIDE CHAINS REBUILT WHERE THERE WAS CLEAR DEVIATION FROM 222 SYMMETRY PART OF THE FOLLOWING SIDE CHAINS HAS BEEN OMITTED:- A 50, A 51, A 75, A 77, A 79, A 80, A 83, A 84, A 90, A 111, A 162, A 171, A 195, A 200, A 214, A 303, B 50, B 75, B 77, B 79, B 80, B 83, B 90, B 91, B 171, B 214, B 232, B 236, B 303. THERE IS NO RESIDUE 302: RESIDUES 303 - 320 HAVE BEEN NUMBERED TO MATCH EQUIVALENT RESIDUES IN E.COLI PFK.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.02 %
Crystal growpH: 7.8
Details: THE CRYSTALS WERE GROWN FROM 1.6 - 1.8M POTASSIUM TARTRATE, PH 7.8, WITH 10MM 2-PHOSPHOGLYCOLATE, 0.5MM EDTA, 0.5MM DTT. THE CRYSTALS WERE GROWN FROM 1.6 - 1.8M POTASSIUM TARTRATE, PH 7.8, ...Details: THE CRYSTALS WERE GROWN FROM 1.6 - 1.8M POTASSIUM TARTRATE, PH 7.8, WITH 10MM 2-PHOSPHOGLYCOLATE, 0.5MM EDTA, 0.5MM DTT. THE CRYSTALS WERE GROWN FROM 1.6 - 1.8M POTASSIUM TARTRATE, PH 7.8, WITH 10MM 2-PHOSPHOGLYCOLATE, 0.5MM EDTA, 0.5MM DTT. 2-PHOSPHOGLYCOLATE IS AN ANALOGUE OF THE NATURAL ALLOSTERIC INHIBITOR PHOSPHOENOLPYRUVATE, SO THIS STRUCTURE REPRESENTS THE ALLOSTERICALLY INHIBITED T-STATE. THE ASYMMETRIC UNIT OF THE CRYSTAL IS THE TETRAMER WHICH OCCURS IN SOLUTION - CHAINS A, B, C, D.
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.6-1.8 Mpotassium tartrate11
210 mMPGC11
30.5 mMEDTA11
40.5 mMDTT11
59-6 mg/mlprotain11

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 44349 / % possible obs: 97 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.126

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
RefinementResolution: 2.6→15 Å
Details: DERIVED FROM ENGH & HUBER PARAMETERS BY V. LAMZIN FINAL RMS COORD. SHIFT 0.0095 ANGSTROMS
RfactorNum. reflection% reflection
Rfree0.255 -5 %
Rwork0.188 --
obs-41947 97 %
Displacement parametersBiso mean: 33 Å2
Refinement stepCycle: LAST / Resolution: 2.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9395 0 36 226 9657
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0110.02
X-RAY DIFFRACTIONp_angle_d0.0390.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0390.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.53
X-RAY DIFFRACTIONp_mcangle_it3.95
X-RAY DIFFRACTIONp_scbond_it4.14
X-RAY DIFFRACTIONp_scangle_it66
X-RAY DIFFRACTIONp_plane_restr0.010.02
X-RAY DIFFRACTIONp_chiral_restr0.1280.15
X-RAY DIFFRACTIONp_singtor_nbd0.1890.3
X-RAY DIFFRACTIONp_multtor_nbd0.2660.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1860.3
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.188 / Rfactor Rfree: 0.255
Solvent computation
*PLUS
Displacement parameters
*PLUS

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