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- PDB-6ilr: Structure of Arabidopsis thaliana Ribokinase in unligand form -

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Basic information

Entry
Database: PDB / ID: 6ilr
TitleStructure of Arabidopsis thaliana Ribokinase in unligand form
ComponentsRibokinase
KeywordsTRANSFERASE / Ribose / Ribokinase / AtRBSK / PfkB family / Phosphotransferase
Function / homology
Function and homology information


plastid nucleoid / chloroplast nucleoid / ribokinase / ribokinase activity / nucleoside metabolic process / D-ribose catabolic process / chloroplast stroma / chloroplast / ATP binding / metal ion binding / nucleus
Similarity search - Function
Ribokinase / Ribokinase/fructokinase / pfkB family of carbohydrate kinases signature 2. / Carbohydrate/purine kinase, PfkB, conserved site / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.972 Å
AuthorsKang, P. / Oh, J. / Rhee, S.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
Rural Development AdministrationPJ01325801 Korea, Republic Of
National Research Foundation (Korea)2017R1A2B4002860 Korea, Republic Of
CitationJournal: J. Struct. Biol. / Year: 2019
Title: Crystal structure and mutational analyses of ribokinase from Arabidopsis thaliana.
Authors: Kang, P.A. / Oh, J. / Lee, H. / Witte, C.P. / Rhee, S.
History
DepositionOct 19, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribokinase
B: Ribokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2926
Polymers65,8582
Non-polymers4344
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-26 kcal/mol
Surface area25070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.040, 99.040, 165.458
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Ribokinase / RK


Mass: 32928.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: To make AtRBSK crystal, we deleted 1-67 residues of AtRBSK. The reason for target protein truncation is to remove the disorder. Miss matched sequence Met67 is expression tag. The full-length ...Details: To make AtRBSK crystal, we deleted 1-67 residues of AtRBSK. The reason for target protein truncation is to remove the disorder. Miss matched sequence Met67 is expression tag. The full-length AtRBSK sequence is as follows : >ribokinase.at MMKGISSVSQSINYNPYIEFNRPQLQISTVNPNPAQSRFSRPRSLRVLSLSADPSANRNPKSAVDAHAPPLVVVGSANADIYVEIERLPKEGETISAKTGQTLAGGKGANQAACGAKLMYPTYFVGRLGEDAHGKLIAEALGDDGCGVHLDYVRSVNNEPTGHAVVMLQSDGQNSIIIVGGANMKAWPEIMSDDDLEIVRNAGIVLLQREIPDSINIQVAKAVKKAGVPVILDVGGMDTPIPNELLDSIDILSPNETELSRLTGMPTETFEQISQAVAKCHKLGVKQVLVKLGSKGSALFIQGEKPIQQSIIPAAQVVDTTGAGDTFTAAFAVAMVEGKSHEECLRFAAAAASLCVQVKGAIPSMPDRKSVLKLLKFSI Therefore, N-terminal residues 1-67 were deleted to make AtRBSK crystal.
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g17160, F20D23.14, F20D23_14 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A1A6H3, ribokinase
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 3.08 Å3/Da / Density % sol: 60.07 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.1M sodium citrate (pH 5.5), 40 % (v/v) PEG 600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.972→50 Å / Num. obs: 58558 / % possible obs: 99.8 % / Redundancy: 13 % / CC1/2: 0.999 / Rmerge(I) obs: 0.1 / Net I/σ(I): 23.8
Reflection shellResolution: 1.98→2.05 Å / Rmerge(I) obs: 1.788 / CC1/2: 0.588

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RKD

1rkd


Resolution: 1.972→27.469 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.17
RfactorNum. reflection% reflection
Rfree0.2505 1994 3.41 %
Rwork0.22 --
obs0.2211 58415 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.972→27.469 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4523 0 28 169 4720
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064613
X-RAY DIFFRACTIONf_angle_d0.9236254
X-RAY DIFFRACTIONf_dihedral_angle_d13.31684
X-RAY DIFFRACTIONf_chiral_restr0.034751
X-RAY DIFFRACTIONf_plane_restr0.004814
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.972-2.02130.37251390.3353920X-RAY DIFFRACTION98
2.0213-2.07590.32691400.30463951X-RAY DIFFRACTION100
2.0759-2.1370.32981400.30223965X-RAY DIFFRACTION100
2.137-2.20590.31871410.2894002X-RAY DIFFRACTION100
2.2059-2.28470.37111430.28974011X-RAY DIFFRACTION100
2.2847-2.37610.34511410.28793995X-RAY DIFFRACTION100
2.3761-2.48420.31971400.26924001X-RAY DIFFRACTION100
2.4842-2.61510.34551410.28134019X-RAY DIFFRACTION100
2.6151-2.77880.33141420.2674003X-RAY DIFFRACTION100
2.7788-2.99310.34541420.25854029X-RAY DIFFRACTION99
2.9931-3.29390.26961440.23844051X-RAY DIFFRACTION100
3.2939-3.76950.2341430.20274087X-RAY DIFFRACTION100
3.7695-4.74510.1841470.16584127X-RAY DIFFRACTION100
4.7451-27.47140.18931510.18094260X-RAY DIFFRACTION98

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