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- PDB-6ilt: Structure of Arabidopsis thaliana Ribokinase complexed with ATP a... -

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Basic information

Entry
Database: PDB / ID: 6ilt
TitleStructure of Arabidopsis thaliana Ribokinase complexed with ATP and Magnesium ion
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 / Ribokinase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)67,01510
Polymers65,8582
Non-polymers1,1588
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-68 kcal/mol
Surface area23840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.445, 99.445, 164.952
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-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 3.1 Å3/Da / Density % sol: 60.27 %
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 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 40517 / % possible obs: 93.3 % / Redundancy: 9.3 % / CC1/2: 0.998 / Net I/av σ(I): 19 / Net I/σ(I): 19
Reflection shellResolution: 2.2→2.28 Å / Mean I/σ(I) obs: 1.2 / CC1/2: 0.618

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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

6ilr


Resolution: 2.2→32.343 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.86
RfactorNum. reflection% reflection
Rfree0.2683 1972 4.94 %
Rwork0.2241 --
obs0.2263 39951 91.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→32.343 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4407 0 68 91 4566
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094539
X-RAY DIFFRACTIONf_angle_d1.256204
X-RAY DIFFRACTIONf_dihedral_angle_d15.8041596
X-RAY DIFFRACTIONf_chiral_restr0.046759
X-RAY DIFFRACTIONf_plane_restr0.005800
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1855-2.24010.35251260.31492430X-RAY DIFFRACTION84
2.2401-2.30070.37651370.31232631X-RAY DIFFRACTION90
2.3007-2.36840.41711380.29292645X-RAY DIFFRACTION91
2.3684-2.44480.35131370.27762630X-RAY DIFFRACTION91
2.4448-2.53210.32461390.27112676X-RAY DIFFRACTION92
2.5321-2.63350.33211390.28892680X-RAY DIFFRACTION92
2.6335-2.75330.33551410.27052710X-RAY DIFFRACTION92
2.7533-2.89840.35111410.27782700X-RAY DIFFRACTION92
2.8984-3.07980.34451400.27822704X-RAY DIFFRACTION92
3.0798-3.31740.29231420.25732749X-RAY DIFFRACTION92
3.3174-3.65080.24931350.22122694X-RAY DIFFRACTION91
3.6508-4.17810.26251450.19682743X-RAY DIFFRACTION92
4.1781-5.26040.21811490.17472864X-RAY DIFFRACTION94
5.2604-32.34650.20631630.19613123X-RAY DIFFRACTION97

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