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- PDB-2e2o: Crystal structure of Sulfolobus tokodaii hexokinase in complex wi... -

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Basic information

Entry
Database: PDB / ID: 2e2o
TitleCrystal structure of Sulfolobus tokodaii hexokinase in complex with glucose
ComponentsHEXOKINASE
KeywordsTRANSFERASE / ACETATE AND SUGAR KINASES / HSP70 / ACTIN SUPERFAMILY / RIBONUCLEASE-H FOLD / SUGAR KINASE / GLUCOSE / N-ACETYLGLUCOSAMINE / HEXOKINASE / CONFORMATIONAL CHANGE / PHOSPHORYL TRANSFER
Function / homology
Function and homology information


hexokinase activity / hexokinase / nucleotide binding
Similarity search - Function
: / ATPase, BadF/BadG/BcrA/BcrD type / BadF/BadG/BcrA/BcrD ATPase family / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
beta-D-glucopyranose / ATP-dependent hexokinase
Similarity search - Component
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å
AuthorsNishimasu, H. / Fushinobu, S. / Shoun, H. / Wakagi, T.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Crystal structures of an ATP-dependent hexokinase with broad substrate specificity from the hyperthermophilic archaeon Sulfolobus tokodaii.
Authors: Nishimasu, H. / Fushinobu, S. / Shoun, H. / Wakagi, T.
History
DepositionNov 15, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 16, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 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 1.4Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3372
Polymers32,1571
Non-polymers1801
Water6,756375
1
A: HEXOKINASE
hetero molecules

A: HEXOKINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6754
Polymers64,3142
Non-polymers3602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area4520 Å2
ΔGint-13 kcal/mol
Surface area23570 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)50.806, 77.748, 162.547
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein HEXOKINASE / Hypothetical protein ST2354


Mass: 32157.100 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Plasmid: PET17B / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q96Y14, 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.: 375 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.71 %

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Data collection

Diffraction
IDCrystal-ID
11
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-5A11
SYNCHROTRONPhoton Factory BL-6A20.9790, 0.9795, 0.9686
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDJun 24, 2004
ADSC QUAMTUM 4r2CCDJun 16, 2004
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.9791
30.97951
40.96861
ReflectionResolution: 1.65→50 Å / Num. obs: 38925 / Biso Wilson estimate: 22.5 Å2

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.65→42.53 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1830251.27 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1914 4.9 %RANDOM
Rwork0.188 ---
obs0.188 38755 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.4609 Å2 / ksol: 0.368397 e/Å3
Displacement parametersBiso mean: 24.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å20 Å20 Å2
2--4.3 Å20 Å2
3----5.39 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.65→42.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2257 0 12 375 2644
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.69
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.371.5
X-RAY DIFFRACTIONc_mcangle_it2.982
X-RAY DIFFRACTIONc_scbond_it4.42
X-RAY DIFFRACTIONc_scangle_it6.022.5
LS refinement shellResolution: 1.65→1.75 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.263 321 5.3 %
Rwork0.224 5791 -
obs--94.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3carbohydrate.paramcarbohydrate.top

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