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- PDB-4u1r: ATP-bound structure of human platelet phosphofructokinase in an R... -

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Basic information

Entry
Database: PDB / ID: 4u1r
TitleATP-bound structure of human platelet phosphofructokinase in an R-state, crystal form II
ComponentsATP-dependent 6-phosphofructokinase, platelet type
KeywordsTRANSFERASE / human platelet phosphofructokinase / R-state / allostery / ATP / ADP / F6P / F16BP
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 / 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, conserved site / Phosphofructokinase signature. / Phosphofructokinase domain / 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'-TRIPHOSPHATE / PHOSPHATE ION / ATP-dependent 6-phosphofructokinase, platelet type
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsKloos, M. / Straeter, N.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation 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.
History
DepositionJul 16, 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 5, 2015Group: Database references
Revision 1.3May 8, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _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)327,61620
Polymers324,4474
Non-polymers3,16816
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18390 Å2
ΔGint-118 kcal/mol
Surface area103280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.896, 132.896, 399.105
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 25 - 762 / Label seq-ID: 6 - 743

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

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: 81111.844 Da / Num. of mol.: 4 / Fragment: UNP residues 26-762
Source method: isolated from a genetically manipulated source
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-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 12 / 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: 3.18 Å3/Da / Density % sol: 61.28 % / Description: hexagonal
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1 M MES, 17-23% v/v MPD / 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: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.444
11-h,-k,l20.556
ReflectionResolution: 2.8→50 Å / Num. obs: 101291 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 7.9 % / Biso Wilson estimate: 53.46 Å2 / Rmerge F obs: 0.991 / Rmerge(I) obs: 0.221 / Rrim(I) all: 0.236 / Χ2: 0.896 / Net I/σ(I): 9.53 / Num. measured all: 796444
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
2.8-2.970.5881.2861.7512882316199161221.37399.5
2.97-3.170.7620.8762.5511783515231152300.938100
3.17-3.430.8740.5554.0911213114196141910.593100
3.43-3.750.9490.3396.8110629113080130770.361100
3.75-4.190.9770.19610.779217911932119200.2199.9
4.19-4.830.9890.12616.058470410585105570.13499.7
4.83-5.90.9910.11616.7870997901289700.12499.5
5.9-8.280.9950.0920.5253954712870840.09699.4
8.280.9980.04638.0729530424641400.04997.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation9.26 Å47.01 Å
Translation9.26 Å47.01 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XSCALE2.5.0data scaling
PDB_EXTRACT3.14data extraction
PHASERphasing
Coot0.6.1model building
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→47.01 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.926 / SU B: 14.008 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19825 5117 5.1 %RANDOM
Rwork0.16213 ---
obs0.16392 96167 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 63.145 Å2
Baniso -1Baniso -2Baniso -3
1-12.59 Å20 Å20 Å2
2--12.59 Å20 Å2
3----25.19 Å2
Refinement stepCycle: 1 / Resolution: 2.8→47.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22383 0 184 0 22567
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01922922
X-RAY DIFFRACTIONr_bond_other_d0.0060.0222117
X-RAY DIFFRACTIONr_angle_refined_deg1.471.96531000
X-RAY DIFFRACTIONr_angle_other_deg1.095350720
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.47952921
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.1423.927993
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.588153981
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.40615178
X-RAY DIFFRACTIONr_chiral_restr0.0750.23493
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0226090
X-RAY DIFFRACTIONr_gen_planes_other0.0050.025208
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_it2.7053.72311708
X-RAY DIFFRACTIONr_mcbond_other2.7053.72311707
X-RAY DIFFRACTIONr_mcangle_it4.315.58314621
X-RAY DIFFRACTIONr_mcangle_other4.315.58314622
X-RAY DIFFRACTIONr_scbond_it2.8253.99811214
X-RAY DIFFRACTIONr_scbond_other2.8263.99911203
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5115.88916362
X-RAY DIFFRACTIONr_long_range_B_refined6.75529.61625745
X-RAY DIFFRACTIONr_long_range_B_other6.75529.61625746
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)
11A453290.07
12B453290.07
21A458320.05
22C458320.05
31A449060.08
32D449060.08
41B452490.07
42C452490.07
51B453460.06
52D453460.06
61C448810.08
62D448810.08
LS refinement shellResolution: 2.801→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 361 -
Rwork0.244 6987 -
obs--99.34 %
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)
10.6692-0.2647-0.08291.08740.12540.6536-0.0281-0.0419-0.12480.05250.01770.00630.0901-0.01750.01050.219-0.02390.06760.1682-0.00270.045448.5237214.0561429.0691
20.9142-0.1129-0.12060.83390.18191.1161-0.0272-0.10240.04470.05890.0541-0.2424-0.02450.376-0.02690.1718-0.02110.0220.2513-0.01330.081269.6811237.399411.5471
30.6585-0.3102-0.17971.1040.06670.58140.00530.02320.0452-0.05140.01330.1946-0.0762-0.1569-0.01860.25470.0582-0.07810.2783-0.06830.089511.8313277.0586438.3498
40.6703-0.0507-0.18650.64650.23311.28660.0005-0.02690.1539-0.08410.0286-0.0876-0.39620.1599-0.02910.3691-0.0008-0.05350.2177-0.05090.063441.2737282.735458.6404
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 803
2X-RAY DIFFRACTION2B25 - 803
3X-RAY DIFFRACTION3C25 - 803
4X-RAY DIFFRACTION4D25 - 803

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