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- PDB-5htx: Putative sugar kinases from Arabidopsis thaliana in complex with ADP -

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Basic information

Entry
Database: PDB / ID: 5htx
TitlePutative sugar kinases from Arabidopsis thaliana in complex with ADP
ComponentsPutative xylulose kinase
KeywordsTRANSFERASE / putative sugar kinases / Arabidopsis thaliana / ADP
Function / homology
Function and homology information


D-ribulokinase / D-ribulokinase activity / plastid / chloroplast / ATP binding / cytosol / cytoplasm
Similarity search - Function
Carbohydrate kinase, FGGY, N-terminal / FGGY family of carbohydrate kinases, N-terminal domain / 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 speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.492 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: Data collection / 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

Downloads & links

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Assembly

Deposited unit
A: Putative xylulose kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1842
Polymers47,7571
Non-polymers4271
Water5,260292
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area690 Å2
ΔGint-3 kcal/mol
Surface area17990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.527, 87.486, 53.361
Angle α, β, γ (deg.)90.00, 97.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative xylulose kinase / Xylulose kinase like protein / Xylulose kinase-1


Mass: 47756.930 Da / Num. of mol.: 1 / Fragment: UNP residues 43-478
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: XK-1, At2g21370 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8L794
#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.: 292 / 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: 2.41 Å3/Da / Density % sol: 49.07 %
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: 0.97917 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
ReflectionResolution: 1.49→50 Å / Num. obs: 73256 / % possible obs: 96.3 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 27.37
Reflection shellResolution: 1.49→1.51 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 5.26 / % possible all: 90

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.492→42.835 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.65
RfactorNum. reflection% reflection
Rfree0.172 3432 4.85 %
Rwork0.1434 --
obs0.1448 70724 96.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.492→42.835 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3256 0 27 292 3575
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143357
X-RAY DIFFRACTIONf_angle_d1.4534566
X-RAY DIFFRACTIONf_dihedral_angle_d13.0341226
X-RAY DIFFRACTIONf_chiral_restr0.067511
X-RAY DIFFRACTIONf_plane_restr0.008583
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4919-1.51240.21351350.13442470X-RAY DIFFRACTION89
1.5124-1.5340.18161180.12472643X-RAY DIFFRACTION95
1.534-1.55690.19261370.11412654X-RAY DIFFRACTION95
1.5569-1.58120.16821400.10852633X-RAY DIFFRACTION95
1.5812-1.60710.15311330.10682647X-RAY DIFFRACTION95
1.6071-1.63490.1531330.10572638X-RAY DIFFRACTION96
1.6349-1.66460.1751340.10632694X-RAY DIFFRACTION95
1.6646-1.69660.15171350.11262651X-RAY DIFFRACTION96
1.6966-1.73120.18521360.11812670X-RAY DIFFRACTION96
1.7312-1.76890.16271140.11882721X-RAY DIFFRACTION96
1.7689-1.810.16661380.1222636X-RAY DIFFRACTION96
1.81-1.85530.17341430.11882709X-RAY DIFFRACTION97
1.8553-1.90550.16951240.1252733X-RAY DIFFRACTION97
1.9055-1.96150.17671410.12532666X-RAY DIFFRACTION97
1.9615-2.02480.15461500.12982701X-RAY DIFFRACTION98
2.0248-2.09720.17031410.12972730X-RAY DIFFRACTION98
2.0972-2.18120.1671400.13162729X-RAY DIFFRACTION98
2.1812-2.28040.17861460.14442730X-RAY DIFFRACTION98
2.2804-2.40060.17261470.15062724X-RAY DIFFRACTION98
2.4006-2.5510.18281450.15252749X-RAY DIFFRACTION98
2.551-2.7480.16471430.16312762X-RAY DIFFRACTION99
2.748-3.02440.1811300.17252752X-RAY DIFFRACTION99
3.0244-3.46190.18151490.16622772X-RAY DIFFRACTION99
3.4619-4.3610.171540.15142735X-RAY DIFFRACTION98
4.361-42.85310.16451260.15782743X-RAY DIFFRACTION96

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