[English] 日本語
Yorodumi
- PDB-1pfk: CRYSTAL STRUCTURE OF THE COMPLEX OF PHOSPHOFRUCTOKINASE FROM ESCH... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1pfk
TitleCRYSTAL STRUCTURE OF THE COMPLEX OF PHOSPHOFRUCTOKINASE FROM ESCHERICHIA COLI WITH ITS REACTION PRODUCTS
ComponentsPHOSPHOFRUCTOKINASE
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
ADENOSINE-5'-DIPHOSPHATE / 1,6-di-O-phosphono-beta-D-fructofuranose / ATP-dependent 6-phosphofructokinase isozyme 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsShirakihara, Y. / Evans, P.R.
Citation
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.
#1: Journal: J.Mol.Biol. / Year: 1989
Title: Crystal Structure of Unliganded Phosphofructokinase from Escherichia Coli
Authors: Rypniewski, W.R. / 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: Derived calculations / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / 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_database_status.process_site / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PHOSPHOFRUCTOKINASE
B: PHOSPHOFRUCTOKINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,25612
Polymers69,7702
Non-polymers2,48610
Water4,990277
1
A: PHOSPHOFRUCTOKINASE
B: PHOSPHOFRUCTOKINASE
hetero molecules

A: PHOSPHOFRUCTOKINASE
B: PHOSPHOFRUCTOKINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,51324
Polymers139,5404
Non-polymers4,97320
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area23490 Å2
ΔGint-194 kcal/mol
Surface area41100 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)112.300, 85.400, 77.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given / Matrix: (0.54287, 0.83982), (0.83982, -0.54287), (-1) / Vector: -5.4269)
DetailsTHE CRYSTALLOGRAPHIC ASYMMETRIC UNIT CONTAINS TWO SUBUNITS OF THE TETRAMER. THESE SUBUNITS HAVE BEEN ASSIGNED CHAIN IDENTIFIERS *A* AND *B* AND HAVE DIFFERENT CONFORMATIONS. CHAIN A IS A *CLOSED* SUBUNIT WITH THE MG++ ION BRIDGING THE TWO PRODUCTS. CHAIN B IS AN *OPEN* SUBUNIT WITH THE MG++ BOUND TO ADP ONLY. THERE ARE TWO WATER CHAINS, ONE CORRESPONDING TO EACH SUBUNIT, AND EQUIVALENT WATER MOLECULES IN EACH CHAIN HAVE BEEN ASSIGNED THE SAME RESIDUE NUMBER. THE TETRAMER CAN BE COMPLETED FROM THE DIMER IN THIS ENTRY BY ROTATING 180 DEGREES ABOUT Z (I.E. -X, -Y, Z). THE STORED ORTHOGONAL CRYSTALLOGRAPHIC COORDINATES IN THIS ENTRY MAY BE CONVERTED TO THE MOLECULAR PQR FRAME (WITH THE MOLECULAR DIADS ALONG P,Q,R) BY THE TRANSFORMATION 0.87831 0.47808 0.00000 0.00000 0.00000 0.00000 -1.00000 -2.71300 -0.47808 0.87831 0.00000 0.00000 THE TRANSFORMATION SPECIFIED ON THE *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR THE B CHAIN WHEN APPLIED TO THE A CHAIN. IT WILL ALSO YIELD APPROXIMATE COORDINATES FOR THE A CHAIN WHEN APPLIED TO THE B CHAIN.

-
Components

#1: Protein PHOSPHOFRUCTOKINASE


Mass: 34885.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Cell line: 293 / Strain (production host): 293 / References: UniProt: P0A796, 6-phosphofructokinase
#2: Sugar ChemComp-FBP / 1,6-di-O-phosphono-beta-D-fructofuranose / BETA-FRUCTOSE-1,6-DIPHOSPHATE / FRUCTOSE-1,6-BISPHOSPHATE / 1,6-di-O-phosphono-beta-D-fructose / 1,6-di-O-phosphono-D-fructose / 1,6-di-O-phosphono-fructose


Type: D-saccharide, beta linking / Mass: 340.116 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H14O12P2
IdentifierTypeProgram
b-D-Fruf1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsADP A 324 AND ADP B 324 ARE THE PRODUCTS OF THE CATALYTIC REACTION ATP + F6P --> ADP + F-1,6-DP. ...ADP A 324 AND ADP B 324 ARE THE PRODUCTS OF THE CATALYTIC REACTION ATP + F6P --> ADP + F-1,6-DP. ADP A 326 AND ADP B 326 ARE THE ALLOSTERIC ACTIVATORS.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.56 %
Crystal grow
*PLUS
Method: batch method / pH: 8.3
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
5100 mMTris-HCl11
14 mg/mlprotein11
65 mM11Mgcl2
250 %(v/v)MPD11
30.2 mMfructose 6-pfosphate11
47.5 mMADP11
72.4 mMdithiothreitol11
82.4 mMEDTA11

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 6 Å / Num. obs: 27155 / % possible obs: 74 % / Num. measured all: 93331 / Rmerge(I) obs: 0.133

-
Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.4→100 Å / Rfactor obs: 0.165
Refinement stepCycle: LAST / Resolution: 2.4→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4866 0 152 277 5295
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.008
X-RAY DIFFRACTIONp_angle_d0.03
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
Num. reflection obs: 27127 / Rfactor obs: 0.165
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_planar_d0.050.03
X-RAY DIFFRACTIONp_plane_restr0.020.007
X-RAY DIFFRACTIONp_chiral_restr0.150.105
X-RAY DIFFRACTIONp_mcbond_it32
X-RAY DIFFRACTIONp_scbond_it32.7
X-RAY DIFFRACTIONp_mcangle_it53.3
X-RAY DIFFRACTIONp_scangle_it54.5

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more