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- PDB-1ua4: Crystal Structure of an ADP-dependent Glucokinase from Pyrococcus... -

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Basic information

Entry
Database: PDB / ID: 1ua4
TitleCrystal Structure of an ADP-dependent Glucokinase from Pyrococcus furiosus
ComponentsADP-dependent glucokinase
KeywordsTRANSFERASE / kinase
Function / homology
Function and homology information


ADP-specific glucose/glucosamine kinase / ADP-specific glucokinase activity / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / glucokinase activity / glycolytic process / glucose metabolic process / magnesium ion binding / cytoplasm
Similarity search - Function
ADP-dependent glucose/glucosamine kinase, archaeal / Adenosine kinase, small domain - #20 / ADP-specific phosphofructokinase/glucokinase, archaeal / ADP-specific phosphofructokinase/glucokinase / ADP-specific Phosphofructokinase/Glucokinase conserved region / ADP-dependent kinase (ADPK) domain profile. / Adenosine kinase, small domain / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase ...ADP-dependent glucose/glucosamine kinase, archaeal / Adenosine kinase, small domain - #20 / ADP-specific phosphofructokinase/glucokinase, archaeal / ADP-specific phosphofructokinase/glucokinase / ADP-specific Phosphofructokinase/Glucokinase conserved region / ADP-dependent kinase (ADPK) domain profile. / Adenosine kinase, small domain / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / beta-D-glucopyranose / alpha-D-glucopyranose / ADP-dependent glucose/glucosamine kinase
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsIto, S. / Jeong, J.J. / Yoshioka, I. / Koga, S. / Fushinobu, S. / Shoun, H. / Wakagi, T.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Crystal structure of an ADP-dependent glucokinase from Pyrococcus furiosus: implications for a sugar-induced conformational change in ADP-dependent kinase
Authors: Ito, S. / Fushinobu, S. / Jeong, J.J. / Yoshioka, I. / Koga, S. / Shoun, H. / Wakagi, T.
History
DepositionFeb 27, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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 1.4Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
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: ADP-dependent glucokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0364
Polymers51,3291
Non-polymers7083
Water12,106672
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.677, 88.948, 103.355
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-1542-

HOH

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Components

#1: Protein ADP-dependent glucokinase / glucokinase


Mass: 51328.895 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9V2Z6, glucokinase
#2: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: 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
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 672 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsRESIDUE GLC 1457 AND GBC 2457 ARE IN ALTERNATE CONFORMATIONS OF EACH OTHER.

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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: 41.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: citrate, DTT, glucose, AMP, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 25 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
26 mMADP-beta-S1drop
330 mMglucose1drop
41.6 Mcitrate1reservoirpH6.5
510 mMdithiothreitol1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionHighest resolution: 1.9 Å / Num. obs: 41349 / % possible obs: 99.9 % / Biso Wilson estimate: 11.7 Å2
Reflection
*PLUS
Num. measured all: 167801 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 2.01 Å / Rmerge(I) obs: 0.23

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Processing

SoftwareName: CNS / Version: 1.1 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→28.93 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2501722.17 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.205 2059 5 %RANDOM
Rwork0.168 ---
obs0.168 41206 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.88 Å2 / ksol: 0.384973 e/Å3
Displacement parametersBiso mean: 20.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.9→28.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3611 0 47 672 4330
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.3
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_d0.85
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.21.5
X-RAY DIFFRACTIONc_mcangle_it1.782
X-RAY DIFFRACTIONc_scbond_it2.222
X-RAY DIFFRACTIONc_scangle_it3.332.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.254 318 4.7 %
Rwork0.197 6486 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2FIN4CIS.PARAM
X-RAY DIFFRACTION3AMP_XPLOR_PARAM
X-RAY DIFFRACTION4WATER_REP.PARAM
X-RAY DIFFRACTION5CARBOHYDRATE.PARAM
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 23.9 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.85

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