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- PDB-4wl0: Ligand-free structure of human platelet phosphofructokinase in an... -

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Basic information

Entry
Database: PDB / ID: 4wl0
TitleLigand-free structure of human platelet phosphofructokinase in an R-state, 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 domain / Phosphofructokinase, conserved site / Phosphofructokinase signature. / Phosphofructokinase domain / ATP-dependent 6-phosphofructokinase / Phosphofructokinase superfamily / Phosphofructokinase / Rossmann fold - #450 ...ATP-dependent 6-phosphofructokinase, vertebrate-type / ATP-dependent 6-phosphofructokinase, eukaryotic-type / 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
PHOSPHATE ION / ATP-dependent 6-phosphofructokinase, platelet type
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.89 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 FoundationB8 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: Kloos, M. / Brueser, A. / Kirchberger, J. / Schoeneberg, T. / Straeter, N.
#2: Journal: FASEB J. / Year: 2011
Title: Molecular architecture and structural basis of allosteric regulation of eukaryotic phosphofructokinases.
Authors: Straeter, N. / Marek, S. / Kuettner, E.B. / Kloos, M. / Keim, A. / Brueser, A. / Kirchberger, J. / Schoeneberg, T.
History
DepositionOct 5, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Database references
Revision 1.2Aug 1, 2018Group: Author supporting evidence / Data collection / Database references
Category: diffrn_radiation_wavelength / pdbx_audit_support / pdbx_related_exp_data_set
Item: _pdbx_audit_support.funding_organization
Revision 1.3May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)333,40412
Polymers332,6444
Non-polymers7608
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13060 Å2
ΔGint-82 kcal/mol
Surface area105850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.343, 178.062, 133.117
Angle α, β, γ (deg.)90.000, 104.450, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ALA / End label comp-ID: ALA / Auth seq-ID: 25 - 762 / Label seq-ID: 24 - 761

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB
3chain CCC
4chain DDD
Detailsbiological unit is the same as asym.

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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: truncated humane platelet Pfk plasmid start: mas N-terminal Strep-tag: wshpqfek linker: ga EK-site: ddddk restriction site: vpdpts N-terminal start: aigvl N-terminal start: aa 26 C-terminal end: aa 762
Source: (gene. exp.) Homo sapiens (human) / Gene: PFKP, PFKF / Plasmid: pET51b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta pLysS / References: UniProt: Q01813, 6-phosphofructokinase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.7 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M KCl, 0.025 M MgCl2, 0.05 M Na Cacodylate, 15% iso-Propanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 15, 2013
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: 2.89→50 Å / Num. obs: 79810 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 67.66 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.091 / Χ2: 1.061 / Net I/σ(I): 13.1 / Num. measured all: 289757
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
2.89-3.060.8490.5732.114467612939126880.67698.1
3.06-3.270.9320.3853.334588112149120950.44899.6
3.27-3.530.9710.235.374116311309112760.2799.7
3.53-3.870.9890.138.853691310384103380.15399.6
3.87-4.320.9950.07914.6335238944894260.09399.8
4.32-4.980.9970.05220.9929395837783260.06299.4
4.98-6.080.9970.04824.0226646707370680.05699.9
6.08-8.540.9990.03132.819241550354670.03699.3
8.540.9990.01952.7210604318631260.02398.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4 Å46.97 Å
Translation4 Å46.97 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALE2.5.1data scaling
PHASERphasing
Cootmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
PDB_EXTRACT3.15data extraction
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: unpublished low resolution structure

Resolution: 2.89→46.97 Å / FOM work R set: 0.7776 / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2363 3991 5 %Random selection
Rwork0.2107 75789 --
obs0.212 79780 99.35 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 312.71 Å2 / Biso mean: 96.17 Å2 / Biso min: 39.06 Å2
Refinement stepCycle: final / Resolution: 2.89→46.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22012 0 40 0 22052
Biso mean--93.83 --
Num. residues----2878
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00522394
X-RAY DIFFRACTIONf_angle_d1.09230248
X-RAY DIFFRACTIONf_chiral_restr0.0423420
X-RAY DIFFRACTIONf_plane_restr0.0043924
X-RAY DIFFRACTIONf_dihedral_angle_d15.4628256
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A13140X-RAY DIFFRACTION14.295TORSIONAL
12B13140X-RAY DIFFRACTION14.295TORSIONAL
13C13140X-RAY DIFFRACTION14.295TORSIONAL
14D13140X-RAY DIFFRACTION14.295TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.886-2.91990.39411290.3552444257393
2.9199-2.95550.34671380.33382625276399
2.9555-2.99290.35071340.318925482682100
2.9929-3.03230.32931400.303326562796100
3.0323-3.07390.35121360.299425892725100
3.0739-3.11780.31371380.29492614275299
3.1178-3.16430.34281390.275726502789100
3.1643-3.21370.30381360.275425692705100
3.2137-3.26640.29761390.272426412780100
3.2664-3.32270.31661370.260626142751100
3.3227-3.38310.29191350.256325592694100
3.3831-3.44820.2741400.242726652805100
3.4482-3.51850.28021370.244325942731100
3.5185-3.5950.25411390.237826472786100
3.595-3.67860.23421370.224225992736100
3.6786-3.77060.23931380.20972614275299
3.7706-3.87250.23911360.208925952731100
3.8725-3.98630.21741400.200826472787100
3.9863-4.11490.2221370.187526122749100
4.1149-4.26190.20351380.181626102748100
4.2619-4.43240.21781400.177826612801100
4.4324-4.6340.20751360.171925952731100
4.634-4.87810.16491380.16982623276199
4.8781-5.18330.21151380.179826182756100
5.1833-5.5830.23681390.191826332772100
5.583-6.14370.23271390.207826502789100
6.1437-7.03020.23911380.20082617275599
7.0302-8.84760.19541400.180726592799100
8.8476-46.97710.191400.18152641278199
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)
10.9854-0.2002-0.17511.0580.06932.03050.05510.2683-0.1467-0.2887-0.12740.1140.1609-0.20950.09650.45350.0969-0.00820.6783-0.15960.4853139.5199-23.9184135.4442
22.0667-0.00420.02241.51030.23382.2413-0.12690.10420.4329-0.29640.0968-0.2378-0.67420.17070.04390.57550.0259-0.02040.4405-0.11260.6125152.12416.8927149.3163
30.4705-0.089-0.20750.5296-0.01781.4613-0.11520.0258-0.10810.29620.04120.23450.1711-0.41340.09360.6860.06780.12260.9397-0.09140.5608127.3354-33.7627206.9854
40.86670.29310.1991.36890.11521.7569-0.1217-0.276-0.05180.3524-0.1198-0.23790.20960.27040.25130.62470.2421-0.00270.87220.02790.5063163.3324-34.0233205.6325
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 25 through 802 )A0
2X-RAY DIFFRACTION2chain 'B' and (resid 25 through 802 )B0
3X-RAY DIFFRACTION3chain 'C' and (resid 25 through 802 )C0
4X-RAY DIFFRACTION4chain 'D' and (resid 25 through 802 )D0

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