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- PDB-4xz2: Human platelet phosphofructokinase in an R-state in complex with ... -

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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 6-phosphate metabolic process / canonical glycolysis / monosaccharide binding / fructose 1,6-bisphosphate metabolic process / Glycolysis / AMP binding ...6-phosphofructokinase complex / 6-phosphofructokinase / 6-phosphofructokinase activity / fructose-6-phosphate binding / fructose 6-phosphate metabolic process / canonical glycolysis / monosaccharide binding / fructose 1,6-bisphosphate metabolic process / Glycolysis / AMP binding / cellular response to leukemia inhibitory factor / cadherin binding / protein-containing complex binding / extracellular exosome / ATP binding / identical protein binding / membrane / nucleus / metal ion binding / 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

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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)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

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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: 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

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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: 2.57 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

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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

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Phasing

PhasingMethod: molecular replacement

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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

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