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- PDB-4qs9: Arabidopsis Hexokinase 1 (AtHXK1) mutant S177A structure in gluco... -

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Basic information

Entry
Database: PDB / ID: 4qs9
TitleArabidopsis Hexokinase 1 (AtHXK1) mutant S177A 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 / carbohydrate phosphorylation ...hexose catabolic process / regulation of secondary shoot formation / transpiration / stomatal closure / sugar mediated signaling pathway / hexokinase activity / glucose mediated signaling pathway / hexokinase / fructokinase activity / carbohydrate phosphorylation / plant-type vacuole / glucokinase activity / glucose 6-phosphate metabolic process / programmed cell death / glucose binding / cellular glucose homeostasis / core promoter sequence-specific DNA binding / glycolytic process / glucose metabolic process / mitochondrial outer membrane / regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / zinc ion binding / membrane => GO:0016020 / ATP binding / nucleus / cytosol
Similarity search - Function
Hexokinase; domain 1 / Hexokinase; domain 1 - #20 / Hexokinase domain signature. / Hexokinase, N-terminal / Hexokinase / Hexokinase domain profile. / Hexokinase, binding site / Hexokinase, C-terminal / Hexokinase / Hexokinase ...Hexokinase; domain 1 / Hexokinase; domain 1 - #20 / Hexokinase domain signature. / Hexokinase, N-terminal / Hexokinase / Hexokinase domain profile. / Hexokinase, binding site / Hexokinase, C-terminal / Hexokinase / Hexokinase / 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: 2.103 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

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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)51,9482
Polymers51,7681
Non-polymers1801
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.781, 93.128, 101.797
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: 51768.160 Da / Num. of mol.: 1 / Fragment: UNP residues 30-496 / Mutation: S177A
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 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.04 Å3/Da / Density % sol: 39.72 %
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: 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: 2.1→50 Å / Num. all: 25451 / Num. obs: 25426 / % possible obs: 99.9 % / Observed criterion σ(F): 193613 / Observed criterion σ(I): 193670 / Biso Wilson estimate: 34.65 Å2
Reflection shellResolution: 2.1→2.18 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
Resolution: 2.103→31.623 Å / FOM work R set: 0.7832 / SU ML: 0.23 / σ(F): 1.35 / Phase error: 27.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2347 1303 5.14 %Random
Rwork0.1977 ---
all0.1997 25479 --
obs0.1997 25360 99.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.41 Å2 / Biso mean: 39.6 Å2 / Biso min: 17.87 Å2
Refinement stepCycle: LAST / Resolution: 2.103→31.623 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3365 0 12 100 3477
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053536
X-RAY DIFFRACTIONf_angle_d0.9784797
X-RAY DIFFRACTIONf_chiral_restr0.065563
X-RAY DIFFRACTIONf_plane_restr0.004613
X-RAY DIFFRACTIONf_dihedral_angle_d14.111290
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 (%)
2.1031-2.18720.32321510.25122542269397
2.1872-2.28680.33451250.239226462771100
2.2868-2.40730.28961450.239726492794100
2.4073-2.5580.28511410.237226602801100
2.558-2.75550.32151510.229926422793100
2.7555-3.03250.26451250.231926902815100
3.0325-3.47090.25121450.20527022847100
3.4709-4.37110.19271520.166926992851100
4.3711-31.62670.19021680.16732827299599
Refinement TLS params.Method: refined / Origin x: -10.3241 Å / Origin y: 7.1626 Å / Origin z: -7.0893 Å
111213212223313233
T0.1286 Å20.0022 Å2-0.0241 Å2-0.2076 Å2-0.0335 Å2--0.2035 Å2
L1.2613 °2-0.0159 °2-0.3372 °2-1.4145 °2-0.9556 °2--1.9331 °2
S-0.0041 Å °0.0885 Å °-0.0985 Å °-0.0597 Å °0.0421 Å °0.0457 Å °0.0305 Å °-0.1339 Å °-0.0379 Å °
Refinement TLS groupSelection details: ALL

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