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- PDB-3wx8: Purification, characterization and structure of nucleoside diphos... -

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Basic information

Entry
Database: PDB / ID: 3wx8
TitlePurification, characterization and structure of nucleoside diphosphate kinase from Drosophila S2 cells
ComponentsNucleoside diphosphate kinase
KeywordsTRANSFERASE / nucleotide binding specificity / nuclease activity / Rossmann Fold / catalyzation / NDP Binding / Phosphorylation
Function / homology
Function and homology information


regulation of tube architecture, open tracheal system / Azathioprine ADME / Ribavirin ADME / establishment or maintenance of polarity of follicular epithelium / open tracheal system development / epithelial cell migration, open tracheal system / Interconversion of nucleotide di- and triphosphates / nuclear microtubule / Neutrophil degranulation / nucleoside-diphosphate kinase ...regulation of tube architecture, open tracheal system / Azathioprine ADME / Ribavirin ADME / establishment or maintenance of polarity of follicular epithelium / open tracheal system development / epithelial cell migration, open tracheal system / Interconversion of nucleotide di- and triphosphates / nuclear microtubule / Neutrophil degranulation / nucleoside-diphosphate kinase / nucleotide metabolic process / CTP biosynthetic process / UTP biosynthetic process / adherens junction organization / GTP biosynthetic process / nucleoside diphosphate kinase activity / microtubule-based process / kinase activity / mitotic cell cycle / microtubule binding / microtubule / phosphorylation / GTP binding / magnesium ion binding / ATP binding / plasma membrane / 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
Nucleoside diphosphate kinase
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.952 Å
AuthorsQian, L.
CitationJournal: Protein Expr.Purif. / Year: 2014
Title: Purification, characterization and structure of nucleoside diphosphate kinase from Drosophila melanogaster
Authors: Qian, L. / Liu, X.
History
DepositionJul 25, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase
C: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)51,7053
Polymers51,7053
Non-polymers00
Water11,403633
1
A: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase
C: Nucleoside diphosphate kinase

A: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase
C: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)103,4106
Polymers103,4106
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area16960 Å2
ΔGint-74 kcal/mol
Surface area35560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.243, 114.243, 94.162
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-277-

HOH

21A-349-

HOH

31A-383-

HOH

41C-361-

HOH

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Components

#1: Protein Nucleoside diphosphate kinase / NDK / NDP kinase / Abnormal wing disks protein / Killer of prune protein


Mass: 17234.955 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: awd, K-pn, CG2210 / Production host: Escherichia coli (E. coli) / References: UniProt: P08879, nucleoside-diphosphate kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 633 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.43 Å3/Da / Density % sol: 64.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 60%(v/v) Tacsimate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRF BL17U11
SYNCHROTRONBSRF 1W2B20.9793
Detector
TypeIDDetectorDate
MAR CCD 165 mm1CCDJun 2, 2012
MAR CCD 130 mm2CCDOct 22, 2012
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1YALE MIRRORSSINGLE WAVELENGTHMx-ray1
2YALE MIRRORSSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97931
ReflectionResolution: 1.9→50 Å / Num. obs: 50905 / % possible obs: 99.75 % / Observed criterion σ(F): 10.12 / Observed criterion σ(I): 12.58
Reflection shellHighest resolution: 1.94 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
CNSrefinement
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.952→49.469 Å / FOM work R set: 0.8936 / SU ML: 0.18 / σ(F): 1.34 / Phase error: 16.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.182 2570 5.05 %RANDOM
Rwork0.1549 48304 --
obs0.1563 50874 98.08 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.768 Å2 / ksol: 0.391 e/Å3
Displacement parametersBiso max: 88.31 Å2 / Biso mean: 20.5 Å2 / Biso min: 8.29 Å2
Baniso -1Baniso -2Baniso -3
1--3.5447 Å2-0 Å20 Å2
2---3.5447 Å20 Å2
3---7.0893 Å2
Refinement stepCycle: LAST / Resolution: 1.952→49.469 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3631 0 0 633 4264
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013705
X-RAY DIFFRACTIONf_angle_d1.2535010
X-RAY DIFFRACTIONf_chiral_restr0.086537
X-RAY DIFFRACTIONf_plane_restr0.006639
X-RAY DIFFRACTIONf_dihedral_angle_d14.4581368
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.952-1.98950.2302980.16811837193568
1.9895-2.03010.1831650.15972648281398
2.0301-2.07430.1781420.143726872829100
2.0743-2.12250.17091620.145726882850100
2.1225-2.17560.2081320.142927222854100
2.1756-2.23440.18371640.1426912855100
2.2344-2.30020.19941520.142827022854100
2.3002-2.37440.18441240.146327332857100
2.3744-2.45930.17071150.145727512866100
2.4593-2.55780.19551590.151927042863100
2.5578-2.67420.19161590.158627152874100
2.6742-2.81510.181550.159426982853100
2.8151-2.99150.21431360.17227402876100
2.9915-3.22240.19251230.165727832906100
3.2224-3.54660.16751460.155127462892100
3.5466-4.05960.1631540.137127622916100
4.0596-5.11390.13711420.134427912933100
5.1139-49.48450.22031420.200629063048100

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