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- PDB-1s59: Structure of nucleoside diphosphate kinase 2 with bound dGTP from... -

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Basic information

Entry
Database: PDB / ID: 1s59
TitleStructure of nucleoside diphosphate kinase 2 with bound dGTP from Arabidopsis
ComponentsNucleoside diphosphate kinase IINucleoside-diphosphate kinase
KeywordsTRANSFERASE / kinase
Function / homology
Function and homology information


red, far-red light phototransduction / auxin-activated signaling pathway / thylakoid / nucleoside-diphosphate kinase / chloroplast envelope / CTP biosynthetic process / UTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / plastid ...red, far-red light phototransduction / auxin-activated signaling pathway / thylakoid / nucleoside-diphosphate kinase / chloroplast envelope / CTP biosynthetic process / UTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / plastid / chloroplast stroma / response to UV / chloroplast / response to hydrogen peroxide / phosphorylation / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Nucleoside diphosphate kinase (NDPK)-like domain profile. / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily / Alpha-Beta Plaits ...Nucleoside diphosphate kinase (NDPK)-like domain profile. / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2'-DEOXYGUANOSINE-5'-DIPHOSPHATE / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / Nucleoside diphosphate kinase II, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsIm, Y.J. / Kim, J.-I. / Shen, Y. / Na, Y. / Han, Y.-J. / Kim, S.-H. / Song, P.-S. / Eom, S.H.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Structural analysis of Arabidopsis thaliana nucleoside diphosphate kinase-2 for phytochrome-mediated light signaling
Authors: Im, Y.J. / Kim, J.-I. / Shen, Y. / Na, Y. / Han, Y.-J. / Kim, S.-H. / Song, P.-S. / Eom, S.H.
History
DepositionJan 20, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoside diphosphate kinase II
B: Nucleoside diphosphate kinase II
C: Nucleoside diphosphate kinase II
D: Nucleoside diphosphate kinase II
E: Nucleoside diphosphate kinase II
F: Nucleoside diphosphate kinase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,4248
Polymers102,4906
Non-polymers9342
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18500 Å2
ΔGint-99 kcal/mol
Surface area33940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.035, 108.520, 118.316
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Nucleoside diphosphate kinase II / Nucleoside-diphosphate kinase / nucleoside diphosphate kinase 2 / NDK II / NDP kinase II / NDPK II / NDPK Ia


Mass: 17081.633 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: NDPK2 / Plasmid: pGEX-4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O64903, nucleoside-diphosphate kinase
#2: Chemical ChemComp-DGI / 2'-DEOXYGUANOSINE-5'-DIPHOSPHATE / Deoxyguanosine diphosphate


Type: DNA linking / Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#3: Chemical ChemComp-DGT / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / Deoxyguanosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.14 Å3/Da / Density % sol: 42.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Ammonium Sulfate, dGTP, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 1.127 Å
DetectorType: MAC Science DIP-2030B / Detector: IMAGE PLATE / Date: Oct 22, 2003 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 27836 / Num. obs: 27023 / % possible obs: 95.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Redundancy: 5.5 % / Biso Wilson estimate: 36.4 Å2 / Rmerge(I) obs: 0.123 / Rsym value: 0.123 / Net I/σ(I): 15.4
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.394 / Mean I/σ(I) obs: 3.8 / Num. unique all: 2529 / Rsym value: 0.394 / % possible all: 91.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1S57

1s57


Resolution: 2.6→34.6 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1864833.98 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.282 1306 4.9 %RANDOM
Rwork0.207 ---
all0.209 27023 --
obs0.207 26876 95.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 14.5654 Å2 / ksol: 0.370344 e/Å3
Displacement parametersBiso mean: 19.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.84 Å20 Å20 Å2
2---1.49 Å20 Å2
3----1.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.6→34.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7095 0 58 235 7388
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_mcbond_it1.091.5
X-RAY DIFFRACTIONc_mcangle_it1.772
X-RAY DIFFRACTIONc_scbond_it1.772
X-RAY DIFFRACTIONc_scangle_it2.632.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.361 189 4.5 %
Rwork0.276 3992 -
obs--91.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3DGTP.PARAMDGTP.TOP
X-RAY DIFFRACTION4DGD.PARAMDGD.TOP

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