[English] 日本語
Yorodumi
- PDB-4xz2: Human platelet phosphofructokinase in an R-state in complex with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4xz2
TitleHuman platelet phosphofructokinase in an R-state in complex with ADP and F6P, crystal form I
ComponentsATP-dependent 6-phosphofructokinase, platelet type
KeywordsTRANSFERASE / human platelet phosphofructokinase / fructose 6-phosphate / main regulator of 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 / canonical glycolysis / Glycolysis / cellular response to leukemia inhibitory factor / cadherin binding ...6-phosphofructokinase complex / 6-phosphofructokinase / 6-phosphofructokinase activity / fructose-6-phosphate binding / fructose 1,6-bisphosphate metabolic process / fructose 6-phosphate metabolic process / canonical glycolysis / Glycolysis / cellular response to leukemia inhibitory factor / cadherin binding / protein-containing complex binding / extracellular exosome / ATP binding / metal ion binding / identical protein binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
ATP-dependent 6-phosphofructokinase, vertebrate-type / ATP-dependent 6-phosphofructokinase, eukaryotic-type / Phosphofructokinase, conserved site / Phosphofructokinase signature. / Phosphofructokinase domain / ATP-dependent 6-phosphofructokinase / Phosphofructokinase superfamily / Phosphofructokinase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / 6-O-phosphono-beta-D-fructofuranose / 1,6-di-O-phosphono-beta-D-fructofuranose / PHOSPHATE ION / ATP-dependent 6-phosphofructokinase, platelet type
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.67 Å
Model detailsN- and C-terminal truncation (N=25, C=22 aa), N-terminal Strep-tag and EK-site
AuthorsKloos, M. / Strater, N.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB 610 Germany
Citation
Journal: Biochem.J. / Year: 2015
Title: Crystal structure of human platelet phosphofructokinase-1 locked in an activated conformation.
Authors: Kloos, M. / Bruser, A. / Kirchberger, J. / Schoneberg, T. / Strater, N.
#1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2014
Title: Crystallization and preliminary crystallographic analysis of human muscle phosphofructokinase, the main regulator of glycolysis.
Authors: Brueser, A. / Kirchberger, J. / Schoeneberg, T. / Straeter, N.
History
DepositionFeb 3, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Database references
Revision 1.2Aug 5, 2015Group: Database references
Revision 1.3Jul 29, 2020Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Derived calculations / Structure summary
Category: chem_comp / diffrn_radiation_wavelength ...chem_comp / diffrn_radiation_wavelength / entity / pdbx_audit_support / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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_audit_support.funding_organization / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ATP-dependent 6-phosphofructokinase, platelet type
B: ATP-dependent 6-phosphofructokinase, platelet type
C: ATP-dependent 6-phosphofructokinase, platelet type
D: ATP-dependent 6-phosphofructokinase, platelet type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)335,94918
Polymers332,6444
Non-polymers3,30514
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18410 Å2
ΔGint-106 kcal/mol
Surface area104000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.652, 164.524, 133.200
Angle α, β, γ (deg.)90.00, 102.96, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERAA25 - 76224 - 761
21SERSERBB25 - 76224 - 761
12ALAALAAA26 - 76225 - 761
22ALAALACC26 - 76225 - 761
13ALAALAAA26 - 76225 - 761
23ALAALADD26 - 76225 - 761
14ALAALABB26 - 76225 - 761
24ALAALACC26 - 76225 - 761
15ALAALABB26 - 76225 - 761
25ALAALADD26 - 76225 - 761
16ALAALACC26 - 76225 - 761
26ALAALADD26 - 76225 - 761

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

#1: Protein
ATP-dependent 6-phosphofructokinase, platelet type / PFK-P / 6-phosphofructokinase type C / Phosphofructo-1-kinase isozyme C / PFK-C / Phosphohexokinase


Mass: 83161.023 Da / Num. of mol.: 4 / Fragment: UNP residues 26-762
Source method: isolated from a genetically manipulated source
Details: N- and C- terminal truncated mutant 25 residues were removed from the N-terminus 22 residues were removed from the C-terminus 1-25 Expression Tag
Source: (gene. exp.) Homo sapiens (human) / Gene: PFKP, PFKF / Plasmid: pET51b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta pLysS / References: UniProt: Q01813, 6-phosphofructokinase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: 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.: 4 / Source method: obtained synthetically / Formula: C6H14O12P2
IdentifierTypeProgram
b-D-Fruf1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Sugar ChemComp-F6P / 6-O-phosphono-beta-D-fructofuranose / FRUCTOSE-6-PHOSPHATE / 6-O-phosphono-beta-D-fructose / 6-O-phosphono-D-fructose / 6-O-phosphono-fructose


Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13O9P
IdentifierTypeProgram
b-D-Fruf6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.19 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 0.1 M KCl, 0.025 M MgCl2, 0.05 M Na Cacodylate, 15% iso-Propanol
PH range: 5.4-6.4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 6, 2014
RadiationMonochromator: Si-111 crysta / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.67→50 Å / Num. obs: 89992 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 55.81 Å2 / Rmerge F obs: 0.997 / Rmerge(I) obs: 0.1 / Rrim(I) all: 0.112 / Χ2: 1.002 / Net I/σ(I): 13.55 / Num. measured all: 450502
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.67-2.830.70.7452.086964214615141980.83497.1
2.83-3.030.8490.4883.256762213711136490.54699.5
3.03-3.270.9330.2945.26079112771126550.33199.1
3.27-3.580.9780.1749.396202911817118010.19399.9
3.58-40.9910.115.745482710677106340.11199.6
4-4.620.9960.0623.7946451944593850.06899.4
4.62-5.640.9970.04828.3941227799979340.05499.2
5.64-7.920.9980.04430.830661623061880.04999.3
7.920.9990.02845.817252358535480.03299

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
PHASERPhaser 2.5.1phasing
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WLO

4wlo


Resolution: 2.67→46.03 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.903 / SU B: 35.015 / SU ML: 0.312 / Cross valid method: THROUGHOUT / ESU R Free: 0.354 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25515 4500 5 %RANDOM
Rwork0.21634 ---
obs0.21826 85491 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.405 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å21.16 Å2
2--3.68 Å2-0 Å2
3----4.08 Å2
Refinement stepCycle: LAST / Resolution: 2.67→46.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21936 0 196 0 22132
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01922480
X-RAY DIFFRACTIONr_bond_other_d0.0060.0221741
X-RAY DIFFRACTIONr_angle_refined_deg1.481.96730399
X-RAY DIFFRACTIONr_angle_other_deg1.347349863
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.72852851
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.09123.922974
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.361153912
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.06215174
X-RAY DIFFRACTIONr_chiral_restr0.0750.23434
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0225477
X-RAY DIFFRACTIONr_gen_planes_other0.0050.025087
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1644.40211446
X-RAY DIFFRACTIONr_mcbond_other3.1644.40211445
X-RAY DIFFRACTIONr_mcangle_it5.1536.59914283
X-RAY DIFFRACTIONr_mcangle_other5.1536.59914284
X-RAY DIFFRACTIONr_scbond_it3.4494.87511034
X-RAY DIFFRACTIONr_scbond_other3.4464.87511026
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6477.13816105
X-RAY DIFFRACTIONr_long_range_B_refined10.45141.94195807
X-RAY DIFFRACTIONr_long_range_B_other10.45141.9495803
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A417610.11
12B417610.11
21A415770.11
22C415770.11
31A411070.12
32D411070.12
41B412670.12
42C412670.12
51B434590.11
52D434590.11
61C412470.12
62D412470.12
LS refinement shellResolution: 2.673→2.742 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 315 -
Rwork0.332 5975 -
obs--94.2 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.13110.05140.04180.16150.07350.38590.03020.0153-0.0485-0.0431-0.0063-0.0051-0.08740.0811-0.02390.1163-0.0434-0.02560.04360.01780.2741-10.3172163.2453117.5678
20.6395-0.0832-0.05450.16510.09620.06290.02530.0487-0.0591-0.0404-0.07210.1063-0.0431-0.04230.04680.09340.0162-0.07440.0313-0.02130.3502-46.1575165.302118.6105
30.20090.2079-0.32150.3746-0.18930.74310.0139-0.1206-0.12230.0562-0.1216-0.12060.00270.18860.10770.0355-0.0331-0.05180.24160.12070.2354-20.7392171.3764188.8326
40.36490.09650.06760.3484-0.12810.72650.0826-0.08130.04150.0358-0.03660.1271-0.2260.098-0.0460.156-0.09930.03870.0719-0.01490.2578-30.8844203.6598177.1049
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 802
2X-RAY DIFFRACTION2B25 - 804
3X-RAY DIFFRACTION3C26 - 802
4X-RAY DIFFRACTION4D26 - 804

+
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