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- PDB-4qs8: Arabidopsis Hexokinase 1 (AtHXK1) structure in ligand-free form -

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Basic information

Entry
Database: PDB / ID: 4qs8
TitleArabidopsis Hexokinase 1 (AtHXK1) structure in ligand-free form
ComponentsHexokinase-1
KeywordsTRANSFERASE / Hexokinase / ATP-dependent / sugar sensor
Function / homology
Function and homology information


hexose catabolic process / regulation of secondary shoot formation / transpiration / stomatal closure / sugar mediated signaling pathway / hexokinase activity / glucose mediated signaling pathway / hexokinase / fructokinase activity / glucokinase activity ...hexose catabolic process / regulation of secondary shoot formation / transpiration / stomatal closure / sugar mediated signaling pathway / hexokinase activity / glucose mediated signaling pathway / hexokinase / fructokinase activity / glucokinase activity / plant-type vacuole / programmed cell death / D-glucose binding / core promoter sequence-specific DNA binding / glycolytic process / mitochondrial outer membrane / regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / zinc ion binding / ATP binding / nucleus
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
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.798 Å
AuthorsFeng, J. / Zhao, S. / Liu, L.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Biochemical and structural study of Arabidopsis hexokinase 1
Authors: Feng, J. / Zhao, S. / Chen, X. / Wang, W. / Dong, W. / Chen, J. / Shen, J.-R. / Liu, L. / Kuang, T.
History
DepositionJul 3, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Database references
Revision 1.2Nov 8, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hexokinase-1


Theoretical massNumber of molelcules
Total (without water)51,7841
Polymers51,7841
Non-polymers00
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.239, 72.473, 109.059
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hexokinase-1 / Protein GLUCOSE INSENSITIVE 2


Mass: 51784.160 Da / Num. of mol.: 1 / Fragment: UNP residues 30-496
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: HXK1, GIN2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q42525, hexokinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.14 Å3/Da / Density % sol: 42.41 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: HEPES, 22% PEG 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 30, 2013
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.798→50 Å / Num. all: 42158 / Num. obs: 41821 / % possible obs: 99.2 % / Observed criterion σ(F): 582475 / Observed criterion σ(I): 582558 / Biso Wilson estimate: 30.4 Å2
Reflection shellResolution: 1.8→1.86 Å / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QS7

4qs7


Resolution: 1.798→30.18 Å / FOM work R set: 0.845 / SU ML: 0.18 / σ(F): 1.34 / Phase error: 22.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2216 2112 5.06 %Random
Rwork0.1887 ---
all0.1904 42167 --
obs0.1904 41758 99.03 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.66 Å2 / Biso mean: 39.01 Å2 / Biso min: 15.74 Å2
Refinement stepCycle: LAST / Resolution: 1.798→30.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3417 0 0 247 3664
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053593
X-RAY DIFFRACTIONf_angle_d0.994875
X-RAY DIFFRACTIONf_chiral_restr0.067565
X-RAY DIFFRACTIONf_plane_restr0.003628
X-RAY DIFFRACTIONf_dihedral_angle_d13.5291310
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7984-1.84020.30531230.2412566268997
1.8402-1.88620.28211390.222626342773100
1.8862-1.93720.27721380.222626422780100
1.9372-1.99420.23851300.20926302760100
1.9942-2.05850.2341580.203826142772100
2.0585-2.13210.25171260.194526712797100
2.1321-2.21740.22831380.195626112749100
2.2174-2.31830.23471510.196726582809100
2.3183-2.44050.25611430.198526532796100
2.4405-2.59330.22031370.194826652802100
2.5933-2.79340.21021320.197227012833100
2.7934-3.07430.23891590.199326432802100
3.0743-3.51860.22981470.18972696284399
3.5186-4.43080.20591420.16152609275196
4.4308-30.18460.1911490.18082653280293
Refinement TLS params.Method: refined / Origin x: 16.493 Å / Origin y: 16.853 Å / Origin z: 17.9681 Å
111213212223313233
T0.161 Å20.0064 Å20.0182 Å2-0.2086 Å20.0229 Å2--0.1922 Å2
L0.6351 °20.074 °20.0933 °2-1.5071 °20.937 °2--1.2936 °2
S-0.0231 Å °-0.0642 Å °0.0144 Å °0.0207 Å °-0.1018 Å °0.278 Å °-0.0424 Å °-0.1649 Å °0.1011 Å °
Refinement TLS groupSelection details: ALL

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