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- PDB-5hux: Putative sugar kinases from Synechococcus elongatus PCC7942 in co... -

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Basic information

Entry
Database: PDB / ID: 5hux
TitlePutative sugar kinases from Synechococcus elongatus PCC7942 in complex with ADP
ComponentsProbable sugar kinase
KeywordsTRANSFERASE / putative sugar kinases / Synechococcus elongatus PCC7942 / complex / ADP
Function / homology
Function and homology information


D-ribulokinase / D-ribulokinase activity / xylulose metabolic process / D-xylulokinase activity / ATP binding / cytosol
Similarity search - Function
Carbohydrate kinase, FGGY, C-terminal / FGGY family of carbohydrate kinases, C-terminal domain / ATPase, nucleotide binding domain
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / D-ribulose kinase
Similarity search - Component
Biological speciesSynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.96 Å
AuthorsXie, Y. / Li, M. / Chang, W.
CitationJournal: Plos One / Year: 2016
Title: Crystal Structures of Putative Sugar Kinases from Synechococcus Elongatus PCC 7942 and Arabidopsis Thaliana
Authors: Xie, Y. / Li, M. / Chang, W.
History
DepositionJan 27, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable sugar kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7342
Polymers47,3071
Non-polymers4271
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint-1 kcal/mol
Surface area18670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.104, 46.662, 89.394
Angle α, β, γ (deg.)90.00, 90.56, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Probable sugar kinase


Mass: 47307.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (strain PCC 7942) (bacteria)
Strain: PCC 7942 / Gene: Synpcc7942_2462 / Plasmid: PET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q31KC7
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 2.24 Å3/Da / Density % sol: 45.03 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M BIS-TRIS pH 6.5, 20% w/v Polyethylene glycol monomethyl ether 5000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.96→50 Å / Num. obs: 29851 / % possible obs: 99 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 18.8
Reflection shellResolution: 1.96→2.03 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.233 / Mean I/σ(I) obs: 5.75 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementResolution: 1.96→38.345 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.67
RfactorNum. reflection% reflection
Rfree0.2246 2007 6.72 %
Rwork0.1739 --
obs0.1772 29849 98.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.96→38.345 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3275 0 27 293 3595
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053387
X-RAY DIFFRACTIONf_angle_d0.9564631
X-RAY DIFFRACTIONf_dihedral_angle_d14.0421214
X-RAY DIFFRACTIONf_chiral_restr0.034515
X-RAY DIFFRACTIONf_plane_restr0.004603
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9579-2.00680.28081340.20751767X-RAY DIFFRACTION88
2.0068-2.06110.28651410.19831997X-RAY DIFFRACTION99
2.0611-2.12170.25491430.18761981X-RAY DIFFRACTION99
2.1217-2.19020.24741410.17771979X-RAY DIFFRACTION99
2.1902-2.26850.23611460.18341949X-RAY DIFFRACTION98
2.2685-2.35930.23561380.18661979X-RAY DIFFRACTION98
2.3593-2.46670.24631430.18971992X-RAY DIFFRACTION98
2.4667-2.59670.25681430.19121997X-RAY DIFFRACTION99
2.5967-2.75930.24041460.19271995X-RAY DIFFRACTION99
2.7593-2.97230.24961440.18842001X-RAY DIFFRACTION99
2.9723-3.27130.23731480.18492032X-RAY DIFFRACTION100
3.2713-3.74430.22521470.16752031X-RAY DIFFRACTION100
3.7443-4.71610.18981490.14192040X-RAY DIFFRACTION100
4.7161-38.35280.17471440.16142102X-RAY DIFFRACTION100

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