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- PDB-3f5m: Crystal Structure of ATP-Bound Phosphofructokinase from Trypanoso... -

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Basic information

Entry
Database: PDB / ID: 3f5m
TitleCrystal Structure of ATP-Bound Phosphofructokinase from Trypanosoma brucei
Components6-phospho-1-fructokinase (ATP-dependent phosphofructokinase)
KeywordsTRANSFERASE / 6-phospho-1-fructokinase / glycolysis / ATP binding / kinase activity / ATP-binding / Kinase / Nucleotide-binding
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
ADENOSINE-5'-TRIPHOSPHATE / ATP-dependent 6-phosphofructokinase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMcNae, I.W. / Martinez-Oyanedel, J. / Keillor, J.W. / Michels, P.A.M. / Fothergill-Gilmore, L.A. / Walkinshaw, M.D.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: The crystal structure of ATP-bound phosphofructokinase from Trypanosoma brucei reveals conformational transitions different from those of other phosphofructokinases.
Authors: McNae, I.W. / Martinez-Oyanedel, J. / Keillor, J.W. / Michels, P.A. / Fothergill-Gilmore, L.A. / Walkinshaw, M.D.
History
DepositionNov 4, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 6-phospho-1-fructokinase (ATP-dependent phosphofructokinase)
B: 6-phospho-1-fructokinase (ATP-dependent phosphofructokinase)
C: 6-phospho-1-fructokinase (ATP-dependent phosphofructokinase)
D: 6-phospho-1-fructokinase (ATP-dependent phosphofructokinase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,84718
Polymers214,3734
Non-polymers2,47414
Water7,710428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24950 Å2
ΔGint-198 kcal/mol
Surface area65660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.578, 117.570, 176.587
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 10:45 OR RESSEQ 55:66 OR RESSEQ 72:333 OR RESSEQ 338:482 )
211CHAIN B AND (RESSEQ 10:45 OR RESSEQ 55:66 OR RESSEQ 72:333 OR RESSEQ 338:482 )
311CHAIN C AND (RESSEQ 10:45 OR RESSEQ 55:66 OR RESSEQ 72:333 OR RESSEQ 338:482 )
411CHAIN D AND (RESSEQ 10:45 OR RESSEQ 55:66 OR RESSEQ 72:333 OR RESSEQ 338:482 )

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
6-phospho-1-fructokinase (ATP-dependent phosphofructokinase)


Mass: 53593.348 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: O15648, 6-phosphofructokinase

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Non-polymers , 6 types, 442 molecules

#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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 428 / 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: 2.34 Å3/Da / Density % sol: 47.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 2.3-2.7 M sodium formate, 0.1 M sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.896 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 2, 2002
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.896 Å / Relative weight: 1
ReflectionResolution: 2.7→15.88 Å / Num. all: 54525 / Num. obs: 54525 / % possible obs: 97.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 36.15 Å2 / Rsym value: 0.138 / Net I/σ(I): 9.2
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 7872 / Rsym value: 0.554 / % possible all: 97.8

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Processing

SoftwareName: PHENIX / Version: (phenix.refine) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HIG

2hig


Resolution: 2.7→15.879 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 33.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2856 2775 5.1 %Random
Rwork0.2236 ---
obs0.2268 54434 97.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.189 Å2 / ksol: 0.427 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.427 Å20 Å20 Å2
2---0.508 Å2-0 Å2
3---0.081 Å2
Refinement stepCycle: LAST / Resolution: 2.7→15.879 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14207 0 148 428 14783
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00914581
X-RAY DIFFRACTIONf_angle_d1.25919732
X-RAY DIFFRACTIONf_chiral_restr0.0772256
X-RAY DIFFRACTIONf_plane_restr0.0042533
X-RAY DIFFRACTIONf_dihedral_angle_d18.5665420
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3514X-RAY DIFFRACTIONPOSITIONAL
12B3514X-RAY DIFFRACTIONPOSITIONAL0.082
13C3514X-RAY DIFFRACTIONPOSITIONAL0.05
14D3514X-RAY DIFFRACTIONPOSITIONAL0.059
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.74630.36761390.30912547X-RAY DIFFRACTION97
2.7463-2.7960.35031460.28052527X-RAY DIFFRACTION98
2.796-2.84950.33741480.26832521X-RAY DIFFRACTION98
2.8495-2.90730.31981430.25352552X-RAY DIFFRACTION98
2.9073-2.97010.35241380.2482542X-RAY DIFFRACTION98
2.9701-3.03870.33831320.23062588X-RAY DIFFRACTION98
3.0387-3.11420.28011440.22242579X-RAY DIFFRACTION99
3.1142-3.19770.27051400.21542562X-RAY DIFFRACTION98
3.1977-3.2910.28311350.22942575X-RAY DIFFRACTION99
3.291-3.39620.31271460.20172571X-RAY DIFFRACTION99
3.3962-3.51640.25441410.20422593X-RAY DIFFRACTION99
3.5164-3.65550.24371480.18692596X-RAY DIFFRACTION99
3.6555-3.81970.28151570.19552589X-RAY DIFFRACTION99
3.8197-4.0180.26581170.17612617X-RAY DIFFRACTION98
4.018-4.26510.23461290.18392591X-RAY DIFFRACTION98
4.2651-4.58710.25541520.17932603X-RAY DIFFRACTION98
4.5871-5.03530.23851170.18362613X-RAY DIFFRACTION98
5.0353-5.73360.2511370.20632618X-RAY DIFFRACTION97
5.7336-7.1140.27171210.24222642X-RAY DIFFRACTION97
7.114-15.87910.28371450.24022633X-RAY DIFFRACTION94

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