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- PDB-6xio: ADP-dependent kinase complex with fructose-6-phosphate and ADPbetaS -

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Basic information

Entry
Database: PDB / ID: 6xio
TitleADP-dependent kinase complex with fructose-6-phosphate and ADPbetaS
ComponentsADP-dependent phosphofructokinase
KeywordsTRANSFERASE / ancestral protein reconstruction / ADP-dependent sugar kinases family / glucokinase / phosphofructokinase / enzyme evolution
Function / homologyChem-AT4 / 6-O-phosphono-beta-D-fructofuranose
Function and homology information
Biological speciesMethanosarcinales archaeon (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.12 Å
AuthorsMunoz, S. / Gonzalez-Ordenes, F. / Fuentes, N. / Maturana, P. / Herrera-Morande, A. / Villalobos, P. / Castro-Fernandez, V.
Funding support Chile, 3items
OrganizationGrant numberCountry
Comision Nacional Cientifica y Technologica (CONICYT)1150460 Chile
Comision Nacional Cientifica y Technologica (CONICYT)3160332 Chile
Comision Nacional Cientifica y Technologica (CONICYT)EQM 120208 Chile
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Structure of an ancestral ADP-dependent kinase with fructose-6P reveals key residues for binding, catalysis, and ligand-induced conformational changes.
Authors: Munoz, S.M. / Castro-Fernandez, V. / Guixe, V.
History
DepositionJun 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADP-dependent phosphofructokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4964
Polymers57,7691
Non-polymers7283
Water905
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.574, 79.589, 108.574
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein ADP-dependent phosphofructokinase


Mass: 57768.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcinales archaeon (archaea) / Production host: Escherichia coli (E. coli) / References: ADP-specific phosphofructokinase
#2: Chemical ChemComp-AT4 / 5'-O-[(R)-HYDROXY(THIOPHOSPHONOOXY)PHOSPHORYL]ADENOSINE / ADENOSINE 5'-O-(2-THIODIPHOSPHATE)


Mass: 443.267 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O9P2S
#3: 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.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
b-D-Fruf6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.53 Å3/Da / Density % sol: 51.38 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: Protein Condition: F6P 6 mM, mM ADPbs 2.4 mM, MgCl2 7.4 mM , HEPES 25 mM pH 7.8, NaCl 200 mM and 2-mercaptoethanol 1 mM; Reservoir Condition: PEG 20,000 8.4% w/V, MgCl2 0.2M, Sodium citrate 0.1M pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45867 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 6, 2017
RadiationMonochromator: Double Crystal Monochromator - Water-cooled Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45867 Å / Relative weight: 1
ReflectionResolution: 3.12→44.85 Å / Num. obs: 10902 / % possible obs: 98.3 % / Redundancy: 12.4 % / Biso Wilson estimate: 88.84 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.1507 / Rpim(I) all: 0.04486 / Rrim(I) all: 0.1574 / Net I/σ(I): 16.5
Reflection shellResolution: 3.12→3.23 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.841 / Mean I/σ(I) obs: 3.02 / Num. unique obs: 1053 / CC1/2: 0.9 / CC star: 0.973 / Rpim(I) all: 0.2532 / Rrim(I) all: 0.879 / % possible all: 99.53

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
MxCuBEdata collection
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6C8Z

6c8z


Resolution: 3.12→44.85 Å / SU ML: 0.4712 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.2544 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2717 536 5 %
Rwork0.241 10189 -
obs0.2426 10725 98.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 85.77 Å2
Refinement stepCycle: LAST / Resolution: 3.12→44.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3540 0 44 5 3589
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00453652
X-RAY DIFFRACTIONf_angle_d0.74224975
X-RAY DIFFRACTIONf_chiral_restr0.0513579
X-RAY DIFFRACTIONf_plane_restr0.0071630
X-RAY DIFFRACTIONf_dihedral_angle_d18.37281317
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.12-3.430.38711340.32192521X-RAY DIFFRACTION99.55
3.43-3.930.34041420.28442519X-RAY DIFFRACTION99.29
3.93-4.950.24931230.22342539X-RAY DIFFRACTION97.72
4.95-44.850.22961370.21612610X-RAY DIFFRACTION96.93

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