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- PDB-6ils: Structure of Arabidopsis thaliana Ribokinase complexed with Ribos... -

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Basic information

Entry
Database: PDB / ID: 6ils
TitleStructure of Arabidopsis thaliana Ribokinase complexed with Ribose and ATP
ComponentsRibokinase
KeywordsTRANSFERASE / Ribose / Ribokinase / AtRBSK / PfkB family / Phosphotransferase
Function / homology
Function and homology information


plastid nucleoid / chloroplast nucleoid / ribokinase / ribokinase activity / D-ribose catabolic process / nucleoside metabolic 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
ADENOSINE-5'-TRIPHOSPHATE / alpha-D-ribofuranose / Ribokinase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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)67,0687
Polymers65,8582
Non-polymers1,2105
Water7,350408
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-26 kcal/mol
Surface area24670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.460, 99.460, 165.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-681-

HOH

21A-687-

HOH

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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-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Sugar ChemComp-RIB / alpha-D-ribofuranose / alpha-D-ribose / D-ribose / ribose / Ribose


Type: D-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
DRibfaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-ribofuranoseCOMMON NAMEGMML 1.0
a-D-RibfIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
RibSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 408 / 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: 3.11 Å3/Da / Density % sol: 60.47 %
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: Jul 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 84606 / % possible obs: 99.8 % / Redundancy: 13.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.101 / Net I/σ(I): 29.6
Reflection shellResolution: 1.75→1.81 Å / Rmerge(I) obs: 4.303 / CC1/2: 0.427

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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: 6ILR
Resolution: 1.8→31.833 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2511 3827 4.94 %
Rwork0.2162 --
obs0.2179 77479 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→31.833 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4530 0 74 408 5012
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084672
X-RAY DIFFRACTIONf_angle_d1.0966361
X-RAY DIFFRACTIONf_dihedral_angle_d12.7251679
X-RAY DIFFRACTIONf_chiral_restr0.044762
X-RAY DIFFRACTIONf_plane_restr0.005821
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82280.31671380.32262714X-RAY DIFFRACTION100
1.8228-1.84680.32931610.29972642X-RAY DIFFRACTION100
1.8468-1.87210.33691430.30692698X-RAY DIFFRACTION100
1.8721-1.89880.33181470.29312685X-RAY DIFFRACTION100
1.8988-1.92710.3031360.28482699X-RAY DIFFRACTION100
1.9271-1.95730.30571470.27232658X-RAY DIFFRACTION100
1.9573-1.98930.29911280.26782731X-RAY DIFFRACTION100
1.9893-2.02360.26651470.26322677X-RAY DIFFRACTION100
2.0236-2.06040.29271410.24232675X-RAY DIFFRACTION100
2.0604-2.10010.27521360.24712728X-RAY DIFFRACTION100
2.1001-2.14290.28631310.23962699X-RAY DIFFRACTION100
2.1429-2.18950.28721380.23122701X-RAY DIFFRACTION100
2.1895-2.24040.24091350.23892719X-RAY DIFFRACTION100
2.2404-2.29640.2771500.23762700X-RAY DIFFRACTION100
2.2964-2.35850.28131370.23282720X-RAY DIFFRACTION100
2.3585-2.42790.26981560.22652692X-RAY DIFFRACTION100
2.4279-2.50620.28291190.22692739X-RAY DIFFRACTION100
2.5062-2.59570.251380.23322735X-RAY DIFFRACTION100
2.5957-2.69960.32011310.23342742X-RAY DIFFRACTION100
2.6996-2.82240.22761510.2212731X-RAY DIFFRACTION100
2.8224-2.97110.26781510.22122732X-RAY DIFFRACTION100
2.9711-3.15710.26131700.22262715X-RAY DIFFRACTION100
3.1571-3.40060.28371230.20712781X-RAY DIFFRACTION100
3.4006-3.74240.25931270.19052791X-RAY DIFFRACTION100
3.7424-4.28280.20561420.17242805X-RAY DIFFRACTION100
4.2828-5.39160.17521470.1682841X-RAY DIFFRACTION100
5.3916-31.83830.20791570.19462902X-RAY DIFFRACTION97

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