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- PDB-6oid: Redox Regulation of FN3K from Arabidopsis thaliana -

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Basic information

Entry
Database: PDB / ID: 6oid
TitleRedox Regulation of FN3K from Arabidopsis thaliana
ComponentsProtein-ribulosamine 3-kinase, chloroplastic
KeywordsTRANSFERASE / Kinase / Fructosamine-3-Kinase / Small Molecule Kinase / Protein Repair / Phosphotransferase / Deglycation / PLANT PROTEIN
Function / homology
Function and homology information


protein-ribulosamine 3-kinase / protein-ribulosamine 3-kinase activity / chloroplast / kinase activity / mitochondrion / ATP binding
Similarity search - Function
Fructosamine/Ketosamine-3-kinase / Fructosamine kinase / Protein kinase-like domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Protein-ribulosamine 3-kinase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.365 Å
AuthorsWood, Z.A. / Kadirvelraj, R. / Shrestha, S.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: Sci.Signal. / Year: 2020
Title: A redox-active switch in fructosamine-3-kinases expands the regulatory repertoire of the protein kinase superfamily.
Authors: Shrestha, S. / Katiyar, S. / Sanz-Rodriguez, C.E. / Kemppinen, N.R. / Kim, H.W. / Kadirvelraj, R. / Panagos, C. / Keyhaninejad, N. / Colonna, M. / Chopra, P. / Byrne, D.P. / Boons, G.J. / ...Authors: Shrestha, S. / Katiyar, S. / Sanz-Rodriguez, C.E. / Kemppinen, N.R. / Kim, H.W. / Kadirvelraj, R. / Panagos, C. / Keyhaninejad, N. / Colonna, M. / Chopra, P. / Byrne, D.P. / Boons, G.J. / van der Knaap, E. / Eyers, P.A. / Edison, A.S. / Wood, Z.A. / Kannan, N.
History
DepositionApr 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 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

Downloads & links

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Assembly

Deposited unit
A: Protein-ribulosamine 3-kinase, chloroplastic
B: Protein-ribulosamine 3-kinase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,67127
Polymers70,9342
Non-polymers2,73725
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation, Ultracentrifugation - velocity
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11070 Å2
ΔGint-226 kcal/mol
Surface area24690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.860, 163.640, 70.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Protein-ribulosamine 3-kinase, chloroplastic / Fructosamine 3-kinase-related protein / AtFN3K-RP


Mass: 35466.895 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At3g61080, T27I15_170 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9LEW8, protein-ribulosamine 3-kinase

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Non-polymers , 6 types, 114 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 3.2 Å3/Da / Density % sol: 62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 2 M Ammonium sulfate, 0.1 M MES pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→53.504 Å / Num. obs: 38000 / % possible obs: 99.8 % / Redundancy: 14.5 % / CC1/2: 0.999 / Rrim(I) all: 0.157 / Net I/σ(I): 14.3
Reflection shellResolution: 2.37→2.43 Å / Redundancy: 14.6 % / Num. unique obs: 2683 / CC1/2: 0.52 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F7W, 3JR1, and 5IGS
Resolution: 2.365→53.504 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.21
RfactorNum. reflection% reflection
Rfree0.204 1903 5.01 %
Rwork0.175 --
obs0.1765 37988 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.365→53.504 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4574 0 154 89 4817
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094850
X-RAY DIFFRACTIONf_angle_d1.0716567
X-RAY DIFFRACTIONf_dihedral_angle_d15.9961741
X-RAY DIFFRACTIONf_chiral_restr0.068650
X-RAY DIFFRACTIONf_plane_restr0.006834
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3652-2.42440.32961300.28412457X-RAY DIFFRACTION97
2.4244-2.48990.30041340.24792546X-RAY DIFFRACTION100
2.4899-2.56320.26911350.23932548X-RAY DIFFRACTION100
2.5632-2.64590.25721380.22862558X-RAY DIFFRACTION100
2.6459-2.74050.27571360.2232551X-RAY DIFFRACTION100
2.7405-2.85020.2611270.2282583X-RAY DIFFRACTION100
2.8502-2.97990.2711380.21312553X-RAY DIFFRACTION100
2.9799-3.1370.23651380.21182555X-RAY DIFFRACTION100
3.137-3.33350.22041330.19272573X-RAY DIFFRACTION100
3.3335-3.59090.22731350.18132579X-RAY DIFFRACTION100
3.5909-3.95210.17481430.14982609X-RAY DIFFRACTION100
3.9521-4.52380.14411360.13232605X-RAY DIFFRACTION100
4.5238-5.69840.15551340.14112631X-RAY DIFFRACTION100
5.6984-53.51770.2121460.17552737X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.3761-0.07190.27721.5675-1.19112.3304-0.4057-0.4546-0.67420.42980.1249-0.05780.67530.63380.18220.83510.27890.25290.45310.24770.612963.93177.055435.1953
24.18180.23370.35453.00980.53942.97820.13710.1105-0.126-0.132-0.1104-0.2539-0.0023-0.0227-0.04720.4097-0.02170.01340.46110.03350.348763.359520.15119.0246
32.58380.2843-0.12923.2915-0.03591.971-0.03820.46960.0235-0.68290.12680.16130.2151-0.13210.00460.44710.0154-0.07890.48890.04490.452946.373821.95647.9324
42.3892-0.2604-0.2252.055-0.572.0557-0.0131-0.0743-0.05440.10870.19830.38960.121-0.2211-0.00340.39660.0535-0.01120.3580.07230.444641.591423.119719.5088
51.94630.5689-1.11431.2177-0.30771.7715-0.29130.191-0.61940.0273-0.0469-0.13060.26640.34230.07910.48080.07930.08330.43920.02190.588469.7312.330217.8642
63.2127-0.3181-0.18852.69850.69532.6185-0.4857-0.8347-0.13880.480.24990.04790.40490.2247-0.01490.65340.18810.06360.51650.13410.410358.701614.674445.1455
73.4413-0.187-0.75761.6750.33831.9948-0.2038-1.0533-0.01170.35680.2444-0.02610.24160.614-0.12620.64030.1505-0.01190.7424-0.09670.493261.278831.411747.1904
82.6323-0.1357-1.02981.8968-0.35152.50050.0752-0.32010.44660.01640.09130.0179-0.0580.4223-0.17270.38040.07880.00660.4581-0.08320.41660.767737.130936.0376
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 43 )
2X-RAY DIFFRACTION2chain 'A' and (resid 44 through 106 )
3X-RAY DIFFRACTION3chain 'A' and (resid 107 through 147 )
4X-RAY DIFFRACTION4chain 'A' and (resid 148 through 295 )
5X-RAY DIFFRACTION5chain 'B' and (resid 7 through 43 )
6X-RAY DIFFRACTION6chain 'B' and (resid 44 through 106 )
7X-RAY DIFFRACTION7chain 'B' and (resid 107 through 147 )
8X-RAY DIFFRACTION8chain 'B' and (resid 148 through 295 )

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