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- PDB-1un9: Crystal structure of the dihydroxyacetone kinase from C. freundii... -

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Basic information

Entry
Database: PDB / ID: 1un9
TitleCrystal structure of the dihydroxyacetone kinase from C. freundii in complex with AMP-PNP and Mg2+
ComponentsDIHYDROXYACETONE KINASE
KeywordsKINASE / GLYCERONE KINASE / DHA KINASE / DIHYDROXYACETONE KINASE
Function / homology
Function and homology information


glycerone kinase / anaerobic glycerol catabolic process / glycerone kinase activity / lipid binding / ATP binding / metal ion binding / cytosol
Similarity search - Function
Dihydroxyacetone kinase / DhaL domain / DhaK domain / Dak1 domain / DhaK domain profile. / DhaL domain / DhaL domain superfamily / DAK2 domain / DhaL domain profile. / Dak2 ...Dihydroxyacetone kinase / DhaL domain / DhaK domain / Dak1 domain / DhaK domain profile. / DhaL domain / DhaL domain superfamily / DAK2 domain / DhaL domain profile. / Dak2 / : / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Dihydroxyacetone / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Dihydroxyacetone kinase
Similarity search - Component
Biological speciesCITROBACTER FREUNDII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsSiebold, C. / Arnold, I. / Garcia-Alles, L.F. / Baumann, U. / Erni, B.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Crystal Structure of the Citrobacter Freundii Dihydroxyacetone Kinase Reveals an Eight-Stranded Alpha-Helical Barrel ATP-Binding Domain
Authors: Siebold, C. / Arnold, I. / Garcia-Alles, L.F. / Baumann, U. / Erni, B.
History
DepositionSep 8, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DIHYDROXYACETONE KINASE
B: DIHYDROXYACETONE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,98310
Polymers115,6932
Non-polymers1,2908
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)100.788, 124.869, 236.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.05306, 0.9985, -0.01375), (0.99849, -0.05325, -0.01346), (-0.01417, -0.01302, -0.99981)
Vector: -61.43323, 68.94242, 297.64081)

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Components

#1: Protein DIHYDROXYACETONE KINASE / GLYCERONE KINASE / DHA KINASE


Mass: 57846.633 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CITROBACTER FREUNDII (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P45510, glycerone kinase
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-2HA / DIHYDROXYACETONE


Mass: 90.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H6O3

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.33 Å3/Da / Density % sol: 62.77 %
Crystal growpH: 7.5 / Details: pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 1.763
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.763 Å / Relative weight: 1
ReflectionResolution: 3.1→25 Å / Num. obs: 25784 / % possible obs: 87.4 % / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 9.3
Reflection shellResolution: 3.1→3.18 Å / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 6.5 / % possible all: 86

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Processing

SoftwareName: CNS / Version: 1.1 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→25 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.237 --
obs0.237 24503 89.1 %
Rfree--0.39 %
Refinement stepCycle: LAST / Resolution: 3.1→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7904 0 78 0 7982
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
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

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