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- PDB-5htv: Putative sugar kinases from Arabidopsis thaliana in complex with ... -

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Basic information

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


D-ribulokinase / D-ribulokinase activity / plastid / chloroplast / ATP binding / cytoplasm / cytosol
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / D-ribulose kinase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 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

Downloads & links

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Assembly

Deposited unit
A: Putative xylulose kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2632
Polymers47,7571
Non-polymers5061
Water5,837324
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-2 kcal/mol
Surface area17870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.565, 87.454, 53.364
Angle α, β, γ (deg.)90.00, 96.78, 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-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 2.42 Å3/Da / Density % sol: 49.15 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M BIS-TRIS pH 6.5, 20% w/v Polyethylene glycol monomethyl ether 5,000

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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: 1.75→50 Å / Num. obs: 45097 / % possible obs: 99.5 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 16.81
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 4 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 3.3 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→38.395 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.48
RfactorNum. reflection% reflection
Rfree0.2041 1997 4.43 %
Rwork0.1697 --
obs0.1712 45067 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.78→38.395 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3256 0 31 324 3611
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073361
X-RAY DIFFRACTIONf_angle_d1.1454573
X-RAY DIFFRACTIONf_dihedral_angle_d12.7251234
X-RAY DIFFRACTIONf_chiral_restr0.042513
X-RAY DIFFRACTIONf_plane_restr0.005583
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7522-1.7960.25561340.21132957X-RAY DIFFRACTION96
1.796-1.84450.22731460.19573065X-RAY DIFFRACTION99
1.8445-1.89880.23671410.18193077X-RAY DIFFRACTION100
1.8988-1.96010.21921380.17553042X-RAY DIFFRACTION99
1.9601-2.03020.23051480.16883064X-RAY DIFFRACTION99
2.0302-2.11140.17451430.16023043X-RAY DIFFRACTION99
2.1114-2.20750.18461480.1563098X-RAY DIFFRACTION100
2.2075-2.32390.23651320.16073106X-RAY DIFFRACTION100
2.3239-2.46950.22171500.17243066X-RAY DIFFRACTION100
2.4695-2.66010.19971420.17873102X-RAY DIFFRACTION100
2.6601-2.92770.22141400.17873111X-RAY DIFFRACTION100
2.9277-3.35110.20241460.17273104X-RAY DIFFRACTION100
3.3511-4.22120.16821430.15493086X-RAY DIFFRACTION100
4.2212-38.40420.19931460.16683149X-RAY DIFFRACTION99

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