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- PDB-2e2p: Crystal structure of Sulfolobus tokodaii hexokinase in complex wi... -

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Basic information

Entry
Database: PDB / ID: 2e2p
TitleCrystal structure of Sulfolobus tokodaii hexokinase in complex with ADP
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
ADENOSINE-5'-DIPHOSPHATE / ATP-dependent hexokinase
Similarity search - Component
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HEXOKINASE
B: HEXOKINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6958
Polymers64,3142
Non-polymers1,3816
Water8,683482
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5880 Å2
ΔGint-74 kcal/mol
Surface area23380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.683, 50.043, 83.192
Angle α, β, γ (deg.)90.00, 114.80, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe asymmetric unit contains the biological dimer.

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Components

#1: Protein HEXOKINASE / / Hypothetical protein ST2354


Mass: 32157.100 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Plasmid: PET17B / Production host: Escherichia coli (E. coli) / References: UniProt: Q96Y14, hexokinase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 482 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.36 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 6, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 42187 / Biso Wilson estimate: 14 Å2

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2E2O

2e2o


Resolution: 2→41.72 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 85626.99 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1994 5 %RANDOM
Rwork0.183 ---
obs0.183 40266 95.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.6155 Å2 / ksol: 0.390954 e/Å3
Displacement parametersBiso mean: 23.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.49 Å20 Å20.17 Å2
2--5 Å20 Å2
3----3.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2→41.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4490 0 84 482 5056
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
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_d21.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.264 323 4.9 %
Rwork0.219 6269 -
obs--94.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4adphepes.paramadphepes.top

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