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- PDB-6jj7: Crystal structure of OsHXK6-Glc complex -

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Basic information

Entry
Database: PDB / ID: 6jj7
TitleCrystal structure of OsHXK6-Glc complex
ComponentsRice hexokinase 6
KeywordsSTRUCTURAL PROTEIN / hexokinase ATP
Function / homology
Function and homology information


chloroplast outer membrane / hexokinase / fructokinase activity / carbohydrate phosphorylation / glucokinase activity / glucose 6-phosphate metabolic process / D-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 / D-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
beta-D-glucopyranose / Hexokinase-6
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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-Glc 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 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Rice hexokinase 6
C: Rice hexokinase 6
E: Rice hexokinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,8556
Polymers153,3153
Non-polymers5403
Water00
1
A: Rice hexokinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2852
Polymers51,1051
Non-polymers1801
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area380 Å2
ΔGint4 kcal/mol
Surface area19590 Å2
MethodPISA
2
C: Rice hexokinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2852
Polymers51,1051
Non-polymers1801
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area390 Å2
ΔGint4 kcal/mol
Surface area19430 Å2
MethodPISA
3
E: Rice hexokinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2852
Polymers51,1051
Non-polymers1801
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area380 Å2
ΔGint4 kcal/mol
Surface area19570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.569, 131.569, 188.782
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: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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: 3.06 Å3/Da / Density % sol: 59.77 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M lithium sulfate, 0.1 M ADA 6.5, 30% v/v PEG 400, and the additive 29 (C5) from kit Additive ScreenTM HR2-428 (Hampton Research),2mM glucose

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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: Jun 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.9→45.47 Å / Num. obs: 42411 / % possible obs: 100 % / Redundancy: 2 % / Rmerge(I) obs: 0.03132 / Net I/σ(I): 15.15
Reflection shellResolution: 2.9→3.004 Å / Rmerge(I) obs: 0.1454 / Mean I/σ(I) obs: 4.54 / Num. unique obs: 4180

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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: 4QS7

4qs7


Resolution: 2.9→45.47 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.07
RfactorNum. reflection% reflection
Rfree0.248 1997 4.71 %
Rwork0.1996 --
obs0.2019 42411 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.9→45.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10767 0 36 0 10803
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01410989
X-RAY DIFFRACTIONf_angle_d1.4614856
X-RAY DIFFRACTIONf_dihedral_angle_d22.4636591
X-RAY DIFFRACTIONf_chiral_restr0.0731686
X-RAY DIFFRACTIONf_plane_restr0.011935
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.97250.3141420.25142818X-RAY DIFFRACTION99
2.9725-3.05290.27471400.25392883X-RAY DIFFRACTION100
3.0529-3.14270.35721380.25012840X-RAY DIFFRACTION100
3.1427-3.24410.30421430.25282844X-RAY DIFFRACTION100
3.2441-3.360.2831400.24352852X-RAY DIFFRACTION100
3.36-3.49450.27821420.21442848X-RAY DIFFRACTION100
3.4945-3.65350.27841450.20442888X-RAY DIFFRACTION100
3.6535-3.84610.26011400.19622857X-RAY DIFFRACTION100
3.8461-4.08690.22461420.18742871X-RAY DIFFRACTION100
4.0869-4.40230.20091430.17132901X-RAY DIFFRACTION100
4.4023-4.8450.19881470.15962893X-RAY DIFFRACTION100
4.845-5.54520.21361430.1752911X-RAY DIFFRACTION100
5.5452-6.98310.26531440.20862944X-RAY DIFFRACTION100
6.9831-48.78230.21341480.17473066X-RAY DIFFRACTION100

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