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- PDB-6jj8: Crystal structure of OsHXK6-ATP-Mg2+ complex -

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Basic information

Entry
Database: PDB / ID: 6jj8
TitleCrystal structure of OsHXK6-ATP-Mg2+ complex
ComponentsRice hexokinase 6
KeywordsSTRUCTURAL PROTEIN / Hexokinase ATP phosphorylation
Function / homology
Function and homology information


chloroplast outer membrane / hexokinase / fructokinase activity / carbohydrate phosphorylation / glucokinase activity / glucose 6-phosphate metabolic process / glucose binding / intracellular glucose homeostasis / response to glucose / glycolytic process ...chloroplast outer membrane / hexokinase / fructokinase activity / carbohydrate phosphorylation / glucokinase activity / glucose 6-phosphate metabolic process / glucose binding / intracellular glucose homeostasis / response to glucose / glycolytic process / glucose metabolic process / mitochondrion / ATP binding / cytosol
Similarity search - Function
Hexokinase; domain 1 / Hexokinase; domain 1 - #20 / Hexokinase / Hexokinase, binding site / Hexokinase, N-terminal / Hexokinase, C-terminal / Hexokinase / Hexokinase / Hexokinase domain signature. / Hexokinase domain profile. ...Hexokinase; domain 1 / Hexokinase; domain 1 - #20 / Hexokinase / Hexokinase, binding site / Hexokinase, N-terminal / Hexokinase, C-terminal / Hexokinase / Hexokinase / Hexokinase domain signature. / Hexokinase domain profile. / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Hexokinase-6
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHe, C. / Wei, P. / Chen, J. / Wang, H. / Wan, Y. / Zhou, J. / Zhu, Y. / Huang, W. / Yin, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China China
CitationJournal: To Be Published
Title: Crystal structure of OsHXK6-ATP-Mg2+ complex
Authors: He, C. / Wei, P. / Chen, J. / Wang, H. / Wan, Y. / Zhou, J. / Zhu, Y. / Huang, W. / Yin, L.
History
DepositionFeb 25, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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

Downloads & links

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Assembly

Deposited unit
C: Rice hexokinase 6
A: Rice hexokinase 6
B: Rice hexokinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,95412
Polymers153,3153
Non-polymers1,6399
Water0
1
C: Rice hexokinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6514
Polymers51,1051
Non-polymers5463
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area320 Å2
ΔGint-13 kcal/mol
Surface area19410 Å2
MethodPISA
2
A: Rice hexokinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6514
Polymers51,1051
Non-polymers5463
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area320 Å2
ΔGint-13 kcal/mol
Surface area19560 Å2
MethodPISA
3
B: Rice hexokinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6514
Polymers51,1051
Non-polymers5463
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area330 Å2
ΔGint-13 kcal/mol
Surface area19580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.989, 131.989, 185.012
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Rice hexokinase 6 / Hexokinase-2


Mass: 51105.004 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: HXK6, HXK2, Os01g0742500, LOC_Os01g53930, P0439E07.19 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8LQ68, hexokinase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg

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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: 3.03 Å3/Da / Density % sol: 59.46 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 3 mM magnesium chloride, 2 mM ATP (Biosharp) , 0.1 M sodium cacodylate 6.5, 0.2 M magnesium chloride hexahydrate, 50% v/v PEG 200,

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.8→48.62 Å / Num. obs: 46450 / % possible obs: 100 % / Redundancy: 2 % / Rmerge(I) obs: 0.02207 / Net I/σ(I): 21.16
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.09911 / Mean I/σ(I) obs: 6.6 / Num. unique obs: 4559

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JJ7

6jj7


Resolution: 2.8→48.62 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.78
RfactorNum. reflection% reflection
Rfree0.2466 1997 4.3 %
Rwork0.207 --
obs0.2087 46450 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→48.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10767 0 99 0 10866
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711055
X-RAY DIFFRACTIONf_angle_d0.99414961
X-RAY DIFFRACTIONf_dihedral_angle_d21.7216627
X-RAY DIFFRACTIONf_chiral_restr0.0551683
X-RAY DIFFRACTIONf_plane_restr0.0051938
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.870.31661400.2753127X-RAY DIFFRACTION100
2.87-2.94760.34791400.26753120X-RAY DIFFRACTION100
2.9476-3.03430.27141390.26623150X-RAY DIFFRACTION100
3.0343-3.13230.32481450.25683138X-RAY DIFFRACTION100
3.1323-3.24420.32211440.24993138X-RAY DIFFRACTION100
3.2442-3.37410.31791430.2413129X-RAY DIFFRACTION100
3.3741-3.52760.27561380.22863157X-RAY DIFFRACTION100
3.5276-3.71350.28591450.21933166X-RAY DIFFRACTION100
3.7135-3.94610.22811400.19833150X-RAY DIFFRACTION100
3.9461-4.25060.22921420.18723193X-RAY DIFFRACTION100
4.2506-4.6780.19441430.17093180X-RAY DIFFRACTION100
4.678-5.35420.21581470.1733191X-RAY DIFFRACTION100
5.3542-6.74290.2291410.213240X-RAY DIFFRACTION100
6.7429-48.62890.18811500.17073373X-RAY DIFFRACTION100

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