[English] 日本語
Yorodumi
- PDB-9qv4: 1-Phosphofructokinase mutant K95T/G110S from E. coli with bound f... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9qv4
Title1-Phosphofructokinase mutant K95T/G110S from E. coli with bound fructose-1,6-bisphosphate and ADP
Components1-phosphofructokinase
KeywordsTRANSFERASE / fructose / fructose-1-phosphate / fructose-6-phosphate / kinase / FruK / ATP / ADP / 1-phosphofructokinase / fructose-1 / 6-bisphosphate
Function / homology
Function and homology information


1-phosphofructokinase / 1-phosphofructokinase activity / fructose catabolic process / phosphofructokinase activity / ATP binding / cytosol
Similarity search - Function
Fructose 1-phosphate kinase / Tagatose/fructose phosphokinase / pfkB family of carbohydrate kinases signature 1. / pfkB family of carbohydrate kinases signature 2. / Carbohydrate/purine kinase, PfkB, conserved site / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase-like
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / 1,6-di-O-phosphono-beta-D-fructofuranose / : / 1-phosphofructokinase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsZarzycki, J. / Dronsella, B. / Erb, T.J. / Lindner, S.N.
Funding support Germany, 2items
OrganizationGrant numberCountry
Max Planck Society Germany
German Federal Ministry for Education and Research033RC023G Germany
CitationJournal: To Be Published
Title: Structural investigation of gain of function mutations in 1-phosphofructokinase (FruK) of E. coli
Authors: Dronsella, B. / Zarzycki, J. / Satanowski, A. / Bar-Even, A. / Erb, T.J. / Lindner, S.N.
History
DepositionApr 11, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 1-phosphofructokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7397
Polymers33,7921
Non-polymers9476
Water5,296294
1
A: 1-phosphofructokinase
hetero molecules

A: 1-phosphofructokinase
hetero molecules

A: 1-phosphofructokinase
hetero molecules

A: 1-phosphofructokinase
hetero molecules


  • defined by author
  • Evidence: gel filtration, In gel filtration experiments and during purifaction FruK eluted as a tetramer. However, according to PDBePISA only a homodimer should be stable. Note, that FruK was ...Evidence: gel filtration, In gel filtration experiments and during purifaction FruK eluted as a tetramer. However, according to PDBePISA only a homodimer should be stable. Note, that FruK was crystallized in the presence of substrates/products.
  • 139 kDa, 4 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)138,95528
Polymers135,1664
Non-polymers3,78824
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Unit cell
Length a, b, c (Å)63.120, 98.210, 140.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-784-

HOH

-
Components

-
Protein / Sugars , 2 types, 2 molecules A

#1: Protein 1-phosphofructokinase / Fructose 1-phosphate kinase / Fru1PK


Mass: 33791.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: fruK, fpk, b2168, JW2155 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AEW9, 1-phosphofructokinase
#4: 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.: 1 / Source method: obtained synthetically / Formula: C6H14O12P2 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
b-D-Fruf1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

-
Non-polymers , 5 types, 299 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.21 Å3/Da / Density % sol: 61.71 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: The FruK variant K95T/G110S (3.5 mg/mL) in 20 mM MOPS/KOH buffer (pH 7.4) containing 75 mM KCl and 1 M L-proline was mixed in a 1:1 ratio with condition containing 26 % (w/v) pentaerythritol ...Details: The FruK variant K95T/G110S (3.5 mg/mL) in 20 mM MOPS/KOH buffer (pH 7.4) containing 75 mM KCl and 1 M L-proline was mixed in a 1:1 ratio with condition containing 26 % (w/v) pentaerythritol ethoxylate, 75 mM MES (pH 6.5), 150 mM ammonium sulfate, 8 mM fructose-6-phosphate, 4 mM ADP, and 10 mM magnesium chloride. The final drop volume was 0.8 microliters. Before plunge freezing in liquid nitrogen, the crystals were soaked with addintional 20 mM fructose-6-phosphate, 2 mM ADP, 5 mM magnesium chloride for about 1 minute, before glycerol was added as a cryo-protectant to a final concentration of 30% (v/v).

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.55→19.74 Å / Num. obs: 63211 / % possible obs: 99.6 % / Redundancy: 13.4 % / CC1/2: 1 / Rmerge(I) obs: 0.055 / Rrim(I) all: 0.058 / Net I/σ(I): 25.55
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.55-1.590.83145500.8330.8721
1.59-1.630.75245230.8910.7821
1.63-1.680.62644010.9290.651
1.68-1.730.50342570.9610.5221
1.73-1.790.40641540.9720.4211
1.79-1.850.30740250.9850.3191
1.85-1.920.23738470.9910.2471
1.92-20.17837350.9960.1851
2-2.090.14635930.9960.1521
2.09-2.190.10934340.9980.1141
2.19-2.310.0932520.9980.0931
2.31-2.450.07631200.9980.0791
2.45-2.620.06129020.9990.0641
2.62-2.830.0527210.9990.0521
2.83-3.10.0425110.9990.0411
3.1-3.470.032228510.0341
3.47-40.029204610.031
4-4.90.025173210.0261
4.9-6.930.026136110.0271
6.93-19.740.02676210.0271

-
Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
XSCALEdata scaling
XDSdata reduction
PHENIXphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→19.74 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1742 1998 3.16 %
Rwork0.1598 --
obs0.1603 63195 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2339 0 56 294 2689
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072479
X-RAY DIFFRACTIONf_angle_d1.0123386
X-RAY DIFFRACTIONf_dihedral_angle_d14.784921
X-RAY DIFFRACTIONf_chiral_restr0.055391
X-RAY DIFFRACTIONf_plane_restr0.009432
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.590.26481390.23014257X-RAY DIFFRACTION98
1.59-1.630.20721420.20654335X-RAY DIFFRACTION100
1.63-1.680.19321410.1884334X-RAY DIFFRACTION100
1.68-1.730.20031400.17934305X-RAY DIFFRACTION100
1.73-1.80.17171440.1674379X-RAY DIFFRACTION100
1.8-1.870.16391410.15284313X-RAY DIFFRACTION100
1.87-1.950.15071410.15074328X-RAY DIFFRACTION100
1.95-2.060.18511410.15844360X-RAY DIFFRACTION100
2.06-2.180.18211430.15354373X-RAY DIFFRACTION100
2.18-2.350.16761420.1594365X-RAY DIFFRACTION100
2.35-2.590.20911440.16064396X-RAY DIFFRACTION100
2.59-2.960.17891440.15894401X-RAY DIFFRACTION100
2.96-3.730.16151450.15164451X-RAY DIFFRACTION100
3.73-19.740.16091510.15644600X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 31.9684 Å / Origin y: 20.4455 Å / Origin z: 50.0451 Å
111213212223313233
T0.1364 Å2-0.0171 Å2-0.0118 Å2-0.1506 Å20.0257 Å2--0.1554 Å2
L1.0333 °2-0.3002 °20.1405 °2-0.9398 °2-0.4487 °2--1.3931 °2
S-0.0282 Å °0.1085 Å °0.1496 Å °-0.0588 Å °0.0095 Å °-0.0073 Å °-0.134 Å °-0.0045 Å °0.0058 Å °
Refinement TLS groupSelection details: all

+
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