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- PDB-2pfk: THE CRYSTAL STRUCTURE OF UNLIGANDED PHOSPHOFRUCTOKINASE FROM ESCH... -

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Basic information

Entry
Database: PDB / ID: 2pfk
TitleTHE CRYSTAL STRUCTURE OF UNLIGANDED PHOSPHOFRUCTOKINASE FROM ESCHERICHIA COLI
Components6-PHOSPHOFRUCTOKINASE ISOZYME I
KeywordsTRANSFERASE(PHOSPHOTRANSFERASE)
Function / homology
Function and homology information


6-phosphofructokinase complex / 6-phosphofructokinase / ribonucleotide binding / 6-phosphofructokinase activity / fructose-6-phosphate binding / glucose catabolic process / fructose 1,6-bisphosphate metabolic process / fructose 6-phosphate metabolic process / canonical glycolysis / glycolytic process ...6-phosphofructokinase complex / 6-phosphofructokinase / ribonucleotide binding / 6-phosphofructokinase activity / fructose-6-phosphate binding / glucose catabolic process / fructose 1,6-bisphosphate metabolic process / fructose 6-phosphate metabolic process / canonical glycolysis / glycolytic process / GDP binding / protein homotetramerization / magnesium ion binding / ATP binding / identical protein binding / cytoplasm / cytosol
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
: / ATP-dependent 6-phosphofructokinase isozyme 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsRypniewski, W.R. / Evans, P.R.
Citation
Journal: J.Mol.Biol. / Year: 1989
Title: Crystal structure of unliganded phosphofructokinase from Escherichia coli.
Authors: Rypniewski, W.R. / Evans, P.R.
#1: Journal: J.Mol.Biol. / Year: 1988
Title: Crystal Structure of the Complex of Phosphofructokinase from Escherichia Coli with its Reaction Products
Authors: Shirakihara, Y. / Evans, P.R.
#2: Journal: J.Mol.Biol. / Year: 1986
Title: Crystallographic Structure of Allosterically Inhibited Phosphofructokinase at 7 Angstroms Resolution
Authors: Evans, P.R. / Farrants, G.W. / Lawrence, M.C.
#3: Journal: Eur.J.Biochem. / Year: 1985
Title: Nucleotide Sequence and High-Level Expression of the Major Escherichia Coli Phosphofructokinase
Authors: Hellinga, H.W. / Evans, P.R.
#4: Journal: Philos.Trans.R.Soc.London,Ser.B / Year: 1981
Title: Phosphofructokinase. Structure and Control
Authors: Evans, P.R. / Farrants, G.W. / Hudson, P.J.
#5: Journal: Nature / Year: 1979
Title: Structure and Control of Phosphofructokinase from Bacillus Stearothermophilus
Authors: Evans, P.R. / Hudson, P.J.
#6: Journal: Proc.FEBS Meet. / Year: 1978
Title: The Three-Dimensional Structure of Phosphofructokinase from Bacillus Stearothermophilus
Authors: Evans, P.R. / Hudson, P.J.
History
DepositionJan 25, 1988Processing site: BNL
Revision 1.0Jan 9, 1989Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Jun 6, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Source and taxonomy
Category: atom_site / entity_src_gen ...atom_site / entity_src_gen / pdbx_database_status / pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _atom_site.occupancy / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._atom_site.occupancy / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _pdbx_database_status.process_site / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression
Revision 2.1Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 285THE ENTRY COORDINATES ARE NOT PRESENTED IN THE STANDARD CRYSTAL FRAME.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 6-PHOSPHOFRUCTOKINASE ISOZYME I
B: 6-PHOSPHOFRUCTOKINASE ISOZYME I
C: 6-PHOSPHOFRUCTOKINASE ISOZYME I
D: 6-PHOSPHOFRUCTOKINASE ISOZYME I


Theoretical massNumber of molelcules
Total (without water)139,5404
Polymers139,5404
Non-polymers00
Water6,251347
1
A: 6-PHOSPHOFRUCTOKINASE ISOZYME I
B: 6-PHOSPHOFRUCTOKINASE ISOZYME I


Theoretical massNumber of molelcules
Total (without water)69,7702
Polymers69,7702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 6-PHOSPHOFRUCTOKINASE ISOZYME I
D: 6-PHOSPHOFRUCTOKINASE ISOZYME I


Theoretical massNumber of molelcules
Total (without water)69,7702
Polymers69,7702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)177.000, 66.400, 154.000
Angle α, β, γ (deg.)90.00, 118.80, 90.00
Int Tables number5
Space group name H-MC1211
Components on special symmetry positions
IDModelComponents
11B-365-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.04158, 0.99914), (-1), (0.99914, 0.04158)-61.70351, 0.02603, 59.18931
2given(-0.99891, -0.04666), (-1), (-0.04666, 0.99891)80.09368, 41.78273, 1.86952
3given(0.70531, -0.7089), (1), (0.7089, 0.70531)81.24258, 20.87835, 68.07738

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Components

#1: Protein
6-PHOSPHOFRUCTOKINASE ISOZYME I


Mass: 34885.047 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
References: PIR: KIECFA, UniProt: P0A796*PLUS, 6-phosphofructokinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / 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: 2.84 Å3/Da / Density % sol: 56.7 %
Crystal grow
*PLUS
Method: batch method / PH range low: 7.9 / PH range high: 7.7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlenzyme11
214 %(w/v)PEG600011
31.0 M11NaCl
450 mMTris-HCl11

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Data collection

Reflection
*PLUS
Highest resolution: 2.4 Å / Num. obs: 59481 / Num. measured all: 388304 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.6 Å

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.4→100 Å / Rfactor obs: 0.166
Details: THE SPACE GROUP HAS BEEN CONSIDERED AS C 21, I.E. C 2 WITH THE ORIGIN ON A 21 AXIS. THIS IS THE SAME AS P 21 PLUS THE C-CENTERING. THE COORDINATES IN THIS ENTRY ARE IN THE A*, B, C ...Details: THE SPACE GROUP HAS BEEN CONSIDERED AS C 21, I.E. C 2 WITH THE ORIGIN ON A 21 AXIS. THIS IS THE SAME AS P 21 PLUS THE C-CENTERING. THE COORDINATES IN THIS ENTRY ARE IN THE A*, B, C ORTHOGONAL COORDINATE FRAME. THE CRYSTALLOGRAPHIC SYMMETRY OPERATIONS ARE (X, Y, Z), (-X, 1/2+Y, -Z), (1/2+X, 1/2+Y, Z), AND (1/2-X, Y, -Z). THE ASYMMETRIC UNIT CONTAINS TWO HALF-TETRAMERS, I. E. THERE ARE TWO DIFFERENT SORTS OF TETRAMERS WHICH SIT ON DIFFERENT CRYSTALLOGRAPHIC DYAD AXES, AT (-1/4, 0, 0) AND (1/4, 0, 1/2). THUS THERE ARE FOUR DIFFERENT SUBUNITS IN THE UNIT CELL. THESE SUBUNITS HAVE BEEN ASSIGNED CHAIN IDENTIFIERS A, B, C, AND D. SUBUNITS A AND B ARE RELATED BY A PSEUDO-DYAD. THE TRANSFORMATION PRESENTED ON THE *MTRIX 1* RECORDS BELOW WILL YIELD COORDINATES FOR CHAIN B WHEN APPLIED TO CHAIN A AND VICE VERSA. SUBUNITS C AND D ARE RELATED BY A PSEUDO-DYAD. THE TRANSFORMATION PRESENTED ON THE *MTRIX 2* RECORDS BELOW WILL YIELD COORDINATES FOR CHAIN D WHEN APPLIED TO CHAIN C AND VICE VERSA. TO GENERATE A TETRAMER FROM SUBUNITS A AND B ONE MUST APPLY THE FOLLOWING CRYSTALLOGRAPHIC SYMMETRY OPERATION TO THE COORDINATES PRESENTED BELOW FOR CHAINS A AND B - -1.0 0.0 0.0 -77.53963 0.0 1.0 0.0 0.0 0.0 0.0 -1.0 42.68050 TO GENERATE A TETRAMER FROM SUBUNITS C AND D ONE MUST APPLY THE FOLLOWING CRYSTALLOGRAPHIC SYMMETRY OPERATION TO THE COORDINATES PRESENTED BELOW FOR CHAINS C AND D - -1.0 0.0 0.0 77.53963 0.0 1.0 0.0 0.0 0.0 0.0 -1.0 111.28951 THE TETRAMER FORMED FROM SUBUNITS A AND B IS CENTERED AT (-1/4, 0, 0) AND THE TETRAMER FORMED FROM SUBUNITS C AND D IS CENTERED AT (1/4, 20.89/66.4, 1/2). THE SUBUNITS ARE ALL SIMILAR IN CONFORMATION. THE TRANSFORMATION PRESENTED ON THE *MTRIX 3* RECORDS BELOW WILL YIELD COORDINATES FOR CHAIN C WHEN APPLIED TO CHAIN A. ALL OTHER TRANSFORMATIONS BETWEEN CHAINS CAN BE GENERATED FROM THE GIVEN TRANSFORMATIONS.
Refinement stepCycle: LAST / Resolution: 2.4→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9024 0 0 347 9371
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.012
X-RAY DIFFRACTIONp_angle_d0.042
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
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: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.166
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.04
X-RAY DIFFRACTIONp_dihedral_angle_d32
X-RAY DIFFRACTIONp_dihedral_angle_deg
X-RAY DIFFRACTIONp_planar_d0.050.049
X-RAY DIFFRACTIONp_plane_restr0.020.01
X-RAY DIFFRACTIONp_chiral_restr0.150.15
X-RAY DIFFRACTIONp_mcbond_it33.14
X-RAY DIFFRACTIONp_scbond_it34.06
X-RAY DIFFRACTIONp_mcangle_it55
X-RAY DIFFRACTIONp_scangle_it56.59

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