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Yorodumi- PDB-2pfk: THE CRYSTAL STRUCTURE OF UNLIGANDED PHOSPHOFRUCTOKINASE FROM ESCH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pfk | |||||||||
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Title | THE CRYSTAL STRUCTURE OF UNLIGANDED PHOSPHOFRUCTOKINASE FROM ESCHERICHIA COLI | |||||||||
Components | 6-PHOSPHOFRUCTOKINASE ISOZYME I | |||||||||
Keywords | TRANSFERASE(PHOSPHOTRANSFERASE) | |||||||||
Function / homology | Function and homology information 6-phosphofructokinase complex / 6-phosphofructokinase / fructose-6-phosphate binding / 6-phosphofructokinase activity / ribonucleotide binding / glucose catabolic process / fructose 1,6-bisphosphate metabolic process / fructose 6-phosphate metabolic process / monosaccharide binding / canonical glycolysis ...6-phosphofructokinase complex / 6-phosphofructokinase / fructose-6-phosphate binding / 6-phosphofructokinase activity / ribonucleotide binding / glucose catabolic process / fructose 1,6-bisphosphate metabolic process / fructose 6-phosphate metabolic process / monosaccharide binding / canonical glycolysis / AMP binding / glycolytic process / GDP binding / protein homotetramerization / magnesium ion binding / ATP binding / identical protein binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2.4 Å | |||||||||
Authors | Rypniewski, 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 |
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Remark 285 | THE ENTRY COORDINATES ARE NOT PRESENTED IN THE STANDARD CRYSTAL FRAME. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pfk.cif.gz | 239.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pfk.ent.gz | 193.7 KB | Display | PDB format |
PDBx/mmJSON format | 2pfk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pf/2pfk ftp://data.pdbj.org/pub/pdb/validation_reports/pf/2pfk | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | 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 / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.7 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Method: batch method / PH range low: 7.9 / PH range high: 7.7 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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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 |
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Reflection shell | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 2.6 Å |
-Processing
Software | Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 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 step | Cycle: LAST / Resolution: 2.4→100 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.166 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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