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- PDB-5hty: Sugar kinases from Synechococcus elongatus PCC7942-D221A -

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Basic information

Entry
Database: PDB / ID: 5hty
TitleSugar kinases from Synechococcus elongatus PCC7942-D221A
ComponentsProbable sugar kinase
KeywordsTRANSFERASE / sugar kinases / Synechococcus elongatus PCC7942-D221A / mutation
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.815 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 1.1Jun 15, 2016Group: Refinement description
Revision 1.2Mar 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)47,2631
Polymers47,2631
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.887, 47.206, 89.835
Angle α, β, γ (deg.)90.00, 91.58, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Probable sugar kinase


Mass: 47263.227 Da / Num. of mol.: 1 / Mutation: D221A
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

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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: 2.25 Å3/Da / Density % sol: 45.4 %
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: SSRF / Beamline: BL17U / Wavelength: 0.97916 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 10021 / % possible obs: 99.9 % / Redundancy: 7 % / Rmerge(I) obs: 0.143 / Net I/σ(I): 12.94
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 5.48 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.815→32.634 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.22
RfactorNum. reflection% reflection
Rfree0.2453 997 9.96 %
Rwork0.1955 --
obs0.2005 10011 98.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.815→32.634 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3198 0 0 0 3198
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023280
X-RAY DIFFRACTIONf_angle_d0.6354483
X-RAY DIFFRACTIONf_dihedral_angle_d12.3371170
X-RAY DIFFRACTIONf_chiral_restr0.024500
X-RAY DIFFRACTIONf_plane_restr0.003589
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8152-2.96360.34231240.261178X-RAY DIFFRACTION89
2.9636-3.14910.28421420.24561281X-RAY DIFFRACTION100
3.1491-3.3920.2541460.21491301X-RAY DIFFRACTION100
3.392-3.73290.28271430.20741288X-RAY DIFFRACTION100
3.7329-4.27210.24421480.1821304X-RAY DIFFRACTION100
4.2721-5.37850.21341410.17231326X-RAY DIFFRACTION100
5.3785-32.63630.19761530.16611336X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 26.644 Å / Origin y: 4.2683 Å / Origin z: 21.2908 Å
111213212223313233
T0.1831 Å20.0252 Å2-0.023 Å2-0.2146 Å2-0.0114 Å2--0.218 Å2
L0.4876 °20.2341 °2-0.4877 °2-1.0827 °2-0.1685 °2--1.4921 °2
S-0.045 Å °0.0698 Å °-0.0234 Å °-0.1787 Å °-0.0199 Å °0.0135 Å °0.0478 Å °-0.0998 Å °0.0532 Å °
Refinement TLS groupSelection details: ALL

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