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- PDB-5zqt: Crystal structure of Oryza sativa hexokinase 6 -

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Basic information

Entry
Database: PDB / ID: 5zqt
TitleCrystal structure of Oryza sativa hexokinase 6
ComponentsHexokinase-6
KeywordsTRANSFERASE / hexokinase
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / beta-D-glucopyranose / Hexokinase-6
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsMatsudaira, K. / Mochizuki, S. / Yoshida, H. / Kamitori, S. / Akimitsu, K.
CitationJournal: To Be Published
Title: Crystal structure of Oryza sativa hexokinase 6
Authors: Matsudaira, K. / Mochizuki, S. / Yoshida, H. / Kamitori, S. / Akimitsu, K.
History
DepositionApr 20, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 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: Hexokinase-6
B: Hexokinase-6
C: Hexokinase-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,73312
Polymers155,6013
Non-polymers2,1329
Water1,44180
1
A: Hexokinase-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5784
Polymers51,8671
Non-polymers7113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-12 kcal/mol
Surface area18650 Å2
MethodPISA
2
B: Hexokinase-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5784
Polymers51,8671
Non-polymers7113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-11 kcal/mol
Surface area18690 Å2
MethodPISA
3
C: Hexokinase-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5784
Polymers51,8671
Non-polymers7113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-13 kcal/mol
Surface area18740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.600, 131.600, 188.920
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 Hexokinase-6 / Hexokinase-2


Mass: 51867.008 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: HXK6, HXK2, Os01g0742500, LOC_Os01g53930, P0439E07.19 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8LQ68, hexokinase
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 3.03 Å3/Da / Density % sol: 59.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MOPSO, 0.1 M Bis-Tris, 5%w/v PEG20000, 25% w/v Trimethypropane, 1% w/v NDSB195, 0.1 M Spermine tetrahydrochloride, 0.1 M Spermidine trihydrochloride, 0.1 M 1,4-Diaminobutane ...Details: 0.1 M MOPSO, 0.1 M Bis-Tris, 5%w/v PEG20000, 25% w/v Trimethypropane, 1% w/v NDSB195, 0.1 M Spermine tetrahydrochloride, 0.1 M Spermidine trihydrochloride, 0.1 M 1,4-Diaminobutane dihydrochloride, 0.1 M DL-Ornithine monohydrochloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.84→48.79 Å / Num. obs: 45291 / % possible obs: 99.9 % / Redundancy: 11.1 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 30.56
Reflection shellResolution: 2.84→2.91 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.535 / Num. unique obs: 3318 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QS7

4qs7


Resolution: 2.84→48.79 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.898 / SU B: 15.085 / SU ML: 0.286 / Cross valid method: THROUGHOUT / ESU R: 18.351 / ESU R Free: 0.384 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2659 2282 5 %RANDOM
Rwork0.20323 ---
obs0.20638 42967 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.845 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.02 Å2-0 Å2
2--0.02 Å2-0 Å2
3----0.08 Å2
Refinement stepCycle: 1 / Resolution: 2.84→48.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10527 0 132 80 10739
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01910851
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210434
X-RAY DIFFRACTIONr_angle_refined_deg1.1881.98414706
X-RAY DIFFRACTIONr_angle_other_deg0.605323967
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.37951362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.88723.671474
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.61151839
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4861581
X-RAY DIFFRACTIONr_chiral_restr0.0670.21677
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212201
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022421
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.84→2.914 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 159 -
Rwork0.308 3152 -
obs--100 %

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