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- PDB-6qu3: Crystal Structure of Phosphofructokinase from Trypanosoma brucei ... -

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Basic information

Entry
Database: PDB / ID: 6qu3
TitleCrystal Structure of Phosphofructokinase from Trypanosoma brucei in complex with an allosteric inhibitor ctcb360
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-JJ5 / PHOSPHOSERINE / ATP-dependent 6-phosphofructokinase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsMcNae, I.W. / Dornan, J. / Walkinshaw, M.D.
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)225,55317
Polymers223,0594
Non-polymers2,49513
Water7,242402
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23300 Å2
ΔGint-60 kcal/mol
Surface area69810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.154, 150.561, 83.993
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: _ / 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
11LEULEUAA21 - 48541 - 505
21LEULEUBB21 - 48541 - 505
12SERSERAA23 - 48543 - 505
22SERSERCC23 - 48543 - 505
13ALAALAAA19 - 48539 - 505
23ALAALADD19 - 48539 - 505
14SERSERBB23 - 48543 - 505
24SERSERCC23 - 48543 - 505
15LEULEUBB21 - 48541 - 505
25LEULEUDD21 - 48541 - 505
16SERSERCC23 - 48543 - 505
26SERSERDD23 - 48543 - 505

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

#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

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Non-polymers , 5 types, 415 molecules

#2: Chemical
ChemComp-JJ5 / 1-[(3,4-dichlorophenyl)methyl]-7~{H}-pyrrolo[3,2-c]pyridin-4-one


Mass: 293.148 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H10Cl2N2O
#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: Chemical ChemComp-SEP / PHOSPHOSERINE / PHOSPHONOSERINE


Type: L-peptide linking / Mass: 185.072 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8NO6P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / 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: 2.35 Å3/Da / Density % sol: 47.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1M carboxylic acids (sodium formate, ammonium acetate, sodium citrate tribasic dihydrate, sodium potassium tartrate tetrahydrate and sodium oxamate), buffer (0.1 M imidazole; MES ...Details: 0.1M carboxylic acids (sodium formate, ammonium acetate, sodium citrate tribasic dihydrate, sodium potassium tartrate tetrahydrate and sodium oxamate), buffer (0.1 M imidazole; MES monohydrate (acid)) and precipitant mix (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: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.35→69.07 Å / Num. obs: 88344 / % possible obs: 99.89 % / Redundancy: 9.5 % / Net I/σ(I): 10.8
Reflection shellResolution: 2.35→2.434 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3f5m

3f5m


Resolution: 2.35→68.66 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.93 / SU B: 8.872 / SU ML: 0.203 / Cross valid method: THROUGHOUT / ESU R: 0.372 / ESU R Free: 0.245 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24589 4390 5 %RANDOM
Rwork0.20597 ---
obs0.20795 83957 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 68.112 Å2
Baniso -1Baniso -2Baniso -3
1-1.35 Å20 Å20 Å2
2--1.73 Å2-0 Å2
3----3.08 Å2
Refinement stepCycle: 1 / Resolution: 2.35→68.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14025 0 163 402 14590
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01314424
X-RAY DIFFRACTIONr_bond_other_d0.0010.01713724
X-RAY DIFFRACTIONr_angle_refined_deg1.3331.65219519
X-RAY DIFFRACTIONr_angle_other_deg1.1961.5831656
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.42351807
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.64520.243782
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.18152463
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.85215152
X-RAY DIFFRACTIONr_chiral_restr0.0570.21906
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216222
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023146
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_it3.7437.0197261
X-RAY DIFFRACTIONr_mcbond_other3.7417.0187260
X-RAY DIFFRACTIONr_mcangle_it5.53910.5159065
X-RAY DIFFRACTIONr_mcangle_other5.53910.5159066
X-RAY DIFFRACTIONr_scbond_it3.9387.6247163
X-RAY DIFFRACTIONr_scbond_other3.9387.6247164
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.21111.20610455
X-RAY DIFFRACTIONr_long_range_B_refined10.254133.48558945
X-RAY DIFFRACTIONr_long_range_B_other10.256133.53158810
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-IDNCS model detailsAuth asym-IDNumberRms dev position (Å)
111A135650.09
122B135650.09
213A135730.09
224C135730.09
315A137880.09
326D137880.09
417B136960.08
428C136960.08
519B135650.08
5210D135650.08
6111C136620.08
6212D136620.08
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 329 -
Rwork0.298 6128 -
obs--99.8 %

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