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- PDB-4qs7: Arabidopsis Hexokinase 1 (AtHXK1) structure in glucose-bound form -

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Basic information

Entry
Database: PDB / ID: 4qs7
TitleArabidopsis Hexokinase 1 (AtHXK1) structure in glucose-bound 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
beta-D-glucopyranose / Hexokinase-1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 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 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / 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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 8, 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-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9642
Polymers51,7841
Non-polymers1801
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.530, 90.742, 94.446
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: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 1.83 Å3/Da / Density % sol: 32.93 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: HEPES, 22% PEG 3350, 50uM glucose, 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: May 20, 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: 2→50 Å / Num. all: 26533 / Num. obs: 26082 / % possible obs: 98.3 % / Observed criterion σ(F): 132739 / Observed criterion σ(I): 133077 / Biso Wilson estimate: 25.22 Å2
Reflection shellResolution: 2→2.07 Å / % possible all: 91.6

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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: 3o6w

3o6w


Resolution: 2.001→41.89 Å / FOM work R set: 0.8472 / SU ML: 0.21 / σ(F): 1.34 / Phase error: 21.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2219 1319 5.07 %Random
Rwork0.1744 ---
all0.1768 26558 --
obs0.1768 26014 97.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.43 Å2 / Biso mean: 26.66 Å2 / Biso min: 11.01 Å2
Refinement stepCycle: LAST / Resolution: 2.001→41.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3404 0 12 287 3703
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043483
X-RAY DIFFRACTIONf_angle_d0.8294707
X-RAY DIFFRACTIONf_chiral_restr0.057552
X-RAY DIFFRACTIONf_plane_restr0.003599
X-RAY DIFFRACTIONf_dihedral_angle_d12.7611263
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0011-2.08120.27371350.21912451258690
2.0812-2.17590.23881480.18872717286599
2.1759-2.29060.27061570.21982698285598
2.2906-2.43420.24711400.18472770291099
2.4342-2.62210.25181340.18332766290099
2.6221-2.88590.25761610.185127702931100
2.8859-3.30330.21011530.176627752928100
3.3033-4.16130.20061510.14782825297699
4.1613-41.89920.17831400.16242923306397
Refinement TLS params.Method: refined / Origin x: 10.4723 Å / Origin y: 7.0838 Å / Origin z: 8.4843 Å
111213212223313233
T0.1351 Å2-0.0133 Å2-0.0082 Å2-0.139 Å20.017 Å2--0.1515 Å2
L0.4741 °2-0.2018 °2-0.1561 °2-0.6202 °20.4058 °2--0.9825 °2
S-0.0058 Å °-0.0308 Å °-0.0412 Å °0.0125 Å °0.0287 Å °-0.0326 Å °-0.0227 Å °0.0811 Å °-0.0181 Å °
Refinement TLS groupSelection details: ALL

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