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- PDB-5htr: Putative sugar kinases from Arabidopsis thaliana in apo form -

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Basic information

Entry
Database: PDB / ID: 5htr
TitlePutative sugar kinases from Arabidopsis thaliana in apo form
ComponentsPutative xylulose kinase
KeywordsTRANSFERASE / putative sugar kinases / Arabidopsis thaliana / apo form
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
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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

Downloads & links

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Assembly

Deposited unit
A: Putative xylulose kinase


Theoretical massNumber of molelcules
Total (without water)47,7571
Polymers47,7571
Non-polymers00
Water8,863492
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.742, 87.928, 53.590
Angle α, β, γ (deg.)90.00, 96.91, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 492 / 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: 2.45 Å3/Da / Density % sol: 49.8 %
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: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 30128 / % possible obs: 97.1 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.142 / Net I/σ(I): 12.91
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 4.08 / % possible all: 94.5

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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→23.771 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.24
RfactorNum. reflection% reflection
Rfree0.2033 1987 6.6 %
Rwork0.1703 --
obs0.1725 30087 96.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→23.771 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3256 0 0 492 3748
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083328
X-RAY DIFFRACTIONf_angle_d1.0894521
X-RAY DIFFRACTIONf_dihedral_angle_d12.1511224
X-RAY DIFFRACTIONf_chiral_restr0.039507
X-RAY DIFFRACTIONf_plane_restr0.005582
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9977-2.04760.2281480.18511864X-RAY DIFFRACTION91
2.0476-2.1030.2681300.18331970X-RAY DIFFRACTION95
2.103-2.16480.21151300.17851989X-RAY DIFFRACTION95
2.1648-2.23460.23161550.17851964X-RAY DIFFRACTION96
2.2346-2.31440.22511440.1861968X-RAY DIFFRACTION96
2.3144-2.4070.24041360.18051976X-RAY DIFFRACTION97
2.407-2.51650.22921350.19012043X-RAY DIFFRACTION97
2.5165-2.6490.21731440.18711998X-RAY DIFFRACTION97
2.649-2.81470.24541430.1952015X-RAY DIFFRACTION97
2.8147-3.03160.23431440.19452041X-RAY DIFFRACTION98
3.0316-3.3360.20581410.18572043X-RAY DIFFRACTION98
3.336-3.8170.18721460.15312069X-RAY DIFFRACTION99
3.817-4.80250.14431400.1362049X-RAY DIFFRACTION99
4.8025-23.77270.15511510.14132111X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -17.6593 Å / Origin y: 7.2211 Å / Origin z: 175.7709 Å
111213212223313233
T0.039 Å2-0.0127 Å2-0.0059 Å2-0.0301 Å20.0082 Å2--0.0454 Å2
L0.3183 °20.0182 °2-0.0968 °2-0.2127 °20.118 °2--0.4968 °2
S0.0047 Å °-0.0362 Å °-0.0218 Å °-0.0056 Å °0.0141 Å °-0.0073 Å °0.0046 Å °0.0419 Å °-0.0142 Å °
Refinement TLS groupSelection details: ALL

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