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- PDB-5hv7: Putative sugar kinases from Synechococcus elongatus PCC7942 in co... -

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Basic information

Entry
Database: PDB / ID: 5hv7
TitlePutative sugar kinases from Synechococcus elongatus PCC7942 in complex with D-ribulose
ComponentsProbable sugar kinase
KeywordsTRANSFERASE / complex / putative sugar kinases / Synechococcus elongatus PCC7942 / D-ribulose
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
D-ribulose / D-ribulose kinase
Similarity search - Component
Biological speciesSynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 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 28, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 2.0Jul 1, 2020Group: Atomic model / Derived calculations / Category: atom_site / pdbx_struct_oper_list
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id / _pdbx_struct_oper_list.symmetry_operation
Revision 2.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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)47,6073
Polymers47,3071
Non-polymers3002
Water2,576143
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18040 Å2
Unit cell
Length a, b, c (Å)102.633, 47.012, 88.655
Angle α, β, γ (deg.)90.00, 91.44, 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: Sugar ChemComp-RBL / D-ribulose


Type: D-saccharide / Mass: 150.130 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 47.02 %
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: Dec 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 17931 / % possible obs: 99.8 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 19.38
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 4.64 / % 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: 2.35→24.475 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.11
RfactorNum. reflection% reflection
Rfree0.2687 1777 9.97 %
Rwork0.2297 --
obs0.2336 17823 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.35→24.475 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3209 0 20 143 3372
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033310
X-RAY DIFFRACTIONf_angle_d0.6494519
X-RAY DIFFRACTIONf_dihedral_angle_d13.1441178
X-RAY DIFFRACTIONf_chiral_restr0.024505
X-RAY DIFFRACTIONf_plane_restr0.003593
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3445-2.40780.36971330.32061170X-RAY DIFFRACTION96
2.4078-2.47860.33941370.29391242X-RAY DIFFRACTION100
2.4786-2.55850.40651430.28931238X-RAY DIFFRACTION100
2.5585-2.64980.32651350.29121219X-RAY DIFFRACTION100
2.6498-2.75580.34341340.27161225X-RAY DIFFRACTION100
2.7558-2.8810.291350.26851243X-RAY DIFFRACTION100
2.881-3.03270.32911370.26181242X-RAY DIFFRACTION100
3.0327-3.22230.3361390.27341241X-RAY DIFFRACTION100
3.2223-3.47040.28661330.26091210X-RAY DIFFRACTION97
3.4704-3.81850.28061410.2321218X-RAY DIFFRACTION98
3.8185-4.36830.22991260.19941231X-RAY DIFFRACTION98
4.3683-5.49340.18861360.17411260X-RAY DIFFRACTION100
5.4934-24.4760.20071480.16971307X-RAY DIFFRACTION100

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