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- PDB-5htn: putative sugar kinases from Synechococcus elongatus PCC7942-apo form -

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Basic information

Entry
Database: PDB / ID: 5htn
Titleputative sugar kinases from Synechococcus elongatus PCC7942-apo form
ComponentsProbable sugar kinase
KeywordsTRANSFERASE / putative sugar kinases / Synechococcus elongatus PCC7942 / apo form
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
Biological speciesSynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.301 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 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable sugar kinase


Theoretical massNumber of molelcules
Total (without water)47,3071
Polymers47,3071
Non-polymers00
Water5,639313
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)110.190, 49.047, 86.906
Angle α, β, γ (deg.)90.00, 110.25, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-732-

HOH

21A-762-

HOH

31A-789-

HOH

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 2.39 Å3/Da / Density % sol: 48.59 %
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jun 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 18837 / % possible obs: 96.1 % / Redundancy: 7.4 % / Net I/σ(I): 13.09
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.504 / Mean I/σ(I) obs: 4.1 / % possible all: 94.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementResolution: 2.301→32.501 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.84
RfactorNum. reflection% reflection
Rfree0.2276 1882 10 %
Rwork0.1783 --
obs0.1834 18826 96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.301→32.501 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3190 0 0 313 3503
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033272
X-RAY DIFFRACTIONf_angle_d0.6744472
X-RAY DIFFRACTIONf_dihedral_angle_d12.8511169
X-RAY DIFFRACTIONf_chiral_restr0.026498
X-RAY DIFFRACTIONf_plane_restr0.003588
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3007-2.36290.27291380.21341244X-RAY DIFFRACTION93
2.3629-2.43240.26021420.21081277X-RAY DIFFRACTION95
2.4324-2.51090.28021410.20741266X-RAY DIFFRACTION94
2.5109-2.60060.30771420.22271282X-RAY DIFFRACTION95
2.6006-2.70470.25141430.20411293X-RAY DIFFRACTION95
2.7047-2.82770.26491420.20521271X-RAY DIFFRACTION96
2.8277-2.97670.25311430.2171299X-RAY DIFFRACTION96
2.9767-3.16310.24491450.18561314X-RAY DIFFRACTION96
3.1631-3.40710.22331450.16791300X-RAY DIFFRACTION97
3.4071-3.74950.21471460.15841322X-RAY DIFFRACTION97
3.7495-4.2910.19821480.14591328X-RAY DIFFRACTION97
4.291-5.40220.16631510.14661348X-RAY DIFFRACTION98
5.4022-32.50380.19961560.16961400X-RAY DIFFRACTION99

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