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- PDB-6qu4: Crystal Structure of Phosphofructokinase from Trypanosoma brucei ... -

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Basic information

Entry
Database: PDB / ID: 6qu4
TitleCrystal Structure of Phosphofructokinase from Trypanosoma brucei in complex with an allosteric inhibitor ctcb405
ComponentsATP-dependent 6-phosphofructokinase
KeywordsTRANSFERASE / Glycolysis / Inhibitor / Allostery
Function / homology
Function and homology information


6-phosphofructokinase / 6-phosphofructokinase activity / glycosome / fructose 6-phosphate metabolic process / phosphate ion binding / glycolytic process / ATP binding / metal ion binding
Similarity search - Function
Pyrophosphate-dependent phosphofructokinase TP0108-type / 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
CITRIC ACID / Chem-JJ2 / ATP-dependent 6-phosphofructokinase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsMcNae, I.W. / Dornan, J. / Walkinshaw, M.D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Nat Commun / Year: 2021
Title: Fast acting allosteric phosphofructokinase inhibitors block trypanosome glycolysis and cure acute African trypanosomiasis in mice.
Authors: McNae, I.W. / Kinkead, J. / Malik, D. / Yen, L.H. / Walker, M.K. / Swain, C. / Webster, S.P. / Gray, N. / Fernandes, P.M. / Myburgh, E. / Blackburn, E.A. / Ritchie, R. / Austin, C. / Wear, M. ...Authors: McNae, I.W. / Kinkead, J. / Malik, D. / Yen, L.H. / Walker, M.K. / Swain, C. / Webster, S.P. / Gray, N. / Fernandes, P.M. / Myburgh, E. / Blackburn, E.A. / Ritchie, R. / Austin, C. / Wear, M.A. / Highton, A.J. / Keats, A.J. / Vong, A. / Dornan, J. / Mottram, J.C. / Michels, P.A.M. / Pettit, S. / Walkinshaw, M.D.
History
DepositionFeb 26, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 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
B: ATP-dependent 6-phosphofructokinase
C: ATP-dependent 6-phosphofructokinase
D: ATP-dependent 6-phosphofructokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,65316
Polymers223,0594
Non-polymers2,59412
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22530 Å2
ΔGint-64 kcal/mol
Surface area67560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.584, 165.088, 83.384
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERALAALAAA23 - 48543 - 505
21SERSERALAALABB23 - 48543 - 505
12METMETALAALAAA20 - 48540 - 505
22METMETALAALACC20 - 48540 - 505
13ASNASNLEULEUAA22 - 48442 - 504
23ASNASNLEULEUDD22 - 48442 - 504
14SERSERLYSLYSBB23 - 48643 - 506
24SERSERLYSLYSCC23 - 48643 - 506
15SERSERGLUGLUBB23 - 48343 - 503
25SERSERGLUGLUDD23 - 48343 - 503
16ASNASNLEULEUCC22 - 48442 - 504
26ASNASNLEULEUDD22 - 48442 - 504

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
ATP-dependent 6-phosphofructokinase / Phosphofructokinase / Phosphohexokinase


Mass: 55764.707 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: pfk / Production host: Escherichia coli (E. coli) / References: UniProt: O15648, 6-phosphofructokinase
#2: Chemical
ChemComp-JJ2 / 1-[(3,4-dichlorophenyl)methyl]-5-[2-(dimethylamino)ethyl]pyrrolo[3,2-c]pyridin-4-one


Mass: 364.269 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H19Cl2N3O
#3: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O

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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: 2.63 Å3/Da / Density % sol: 53.15 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 0.1M carboxylic acids (sodium formate, ammonium acetate, sodium citrate tribasic dihydrate, sodium 154 potassium tartrate tetrahydrate and sodium oxamate), buffer system 1 (0.1 M imidazole; ...Details: 0.1M carboxylic acids (sodium formate, ammonium acetate, sodium citrate tribasic dihydrate, sodium 154 potassium tartrate tetrahydrate and sodium oxamate), buffer system 1 (0.1 M imidazole; MES 155 monohydrate (acid)) and precipitant mix 3 (40% v/v glycerol; 20% w/v PEG 4000)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9685 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9685 Å / Relative weight: 1
ReflectionResolution: 2.75→48.02 Å / Num. obs: 50992 / % possible obs: 92.98 % / Redundancy: 4 % / Net I/σ(I): 9.5
Reflection shellResolution: 2.75→2.848 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0241refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3f5m

3f5m


Resolution: 2.75→48.02 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.899 / SU B: 42.894 / SU ML: 0.368 / Cross valid method: THROUGHOUT / ESU R Free: 0.397 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25694 2503 4.9 %RANDOM
Rwork0.21843 ---
obs0.22029 48489 93.01 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 62.15 Å2
Baniso -1Baniso -2Baniso -3
1-3.05 Å2-0 Å2-0 Å2
2---8.69 Å20 Å2
3---5.64 Å2
Refinement stepCycle: LAST / Resolution: 2.75→48.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13845 0 172 72 14089
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01314251
X-RAY DIFFRACTIONr_bond_other_d0.0030.01713555
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.65319291
X-RAY DIFFRACTIONr_angle_other_deg1.1991.58331276
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.00151785
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.1720.377769
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.943152427
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.36915147
X-RAY DIFFRACTIONr_chiral_restr0.0570.21888
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215996
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023081
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_it1.3271.5757170
X-RAY DIFFRACTIONr_mcbond_other1.3271.5757169
X-RAY DIFFRACTIONr_mcangle_it2.2422.368945
X-RAY DIFFRACTIONr_mcangle_other2.2422.368946
X-RAY DIFFRACTIONr_scbond_it1.7931.8667080
X-RAY DIFFRACTIONr_scbond_other1.7931.8667081
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8012.7210347
X-RAY DIFFRACTIONr_long_range_B_refined5.97519.50815624
X-RAY DIFFRACTIONr_long_range_B_other5.97519.5115625
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 / Rms dev position: 0.1 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A13359
12B13359
21A13694
22C13694
31A13336
32D13336
41B13392
42C13392
51B13342
52D13342
61C13429
62D13429
LS refinement shellResolution: 2.75→2.821 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 214 -
Rwork0.333 3560 -
obs--94.92 %
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)
11.26450.6252-0.17691.6717-0.30542.96470.05830.21340.0672-0.11760.06670.0728-0.2570.0306-0.1250.09870.0510.00740.8445-0.02660.0103-18.08445.666-33.444
21.3467-0.1931-0.09421.32930.36311.91340.09650.23420.0576-0.0487-0.0022-0.1743-0.12320.4303-0.09420.0898-0.01240.00530.95020.01520.07483.31242.16-21.169
31.5638-0.4446-0.3881.45690.11552.42250.117-0.1230.08010.1539-0.0277-0.0624-0.1460.001-0.08930.1001-0.0446-0.0130.76920.01420.0123-17.03745.71110.418
40.7986-0.1768-0.06711.8031-0.40032.54850.072-0.0468-0.0615-0.0843-0.01020.10710.3158-0.5237-0.06180.0613-0.0958-0.02320.9-0.01680.0376-34.36833.356-1.694
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 485
2X-RAY DIFFRACTION2B23 - 486
3X-RAY DIFFRACTION3C20 - 486
4X-RAY DIFFRACTION4D22 - 484

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