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- PDB-3vgs: Wild-type nucleoside diphosphate kinase derived from Halomonas sp. 593 -

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Basic information

Entry
Database: PDB / ID: 3vgs
TitleWild-type nucleoside diphosphate kinase derived from Halomonas sp. 593
ComponentsNucleoside diphosphate kinase
KeywordsTRANSFERASE / HALOPHILIC / KINASE / FERREDOXIN FOLD / ATP-BINDING / NUCLEOTIDE-BINDING
Function / homology
Function and homology information


nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / nucleoside diphosphate kinase activity / GTP biosynthetic process / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase (NDPK)-like domain profile. / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily / Alpha-Beta Plaits ...Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase (NDPK)-like domain profile. / 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 speciesHalomonas (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsOkazaki, N. / Yonezawa, Y. / Arai, S. / Matsumoto, F. / Tamada, T. / Tokunaga, H. / Ishibashi, M. / Tokunaga, M. / Kuroki, R.
CitationJournal: Protein Sci. / Year: 2012
Title: A structural mechanism for dimeric to tetrameric oligomer conversion in Halomonas sp. nucleoside diphosphate kinase
Authors: Arai, S. / Yonezawa, Y. / Okazaki, N. / Matsumoto, F. / Tamada, T. / Tokunaga, H. / Ishibashi, M. / Blaber, M. / Tokunaga, M. / Kuroki, R.
History
DepositionAug 20, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)30,5682
Polymers30,5682
Non-polymers00
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-11 kcal/mol
Surface area12540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.531, 112.531, 125.981
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Nucleoside diphosphate kinase / NDK / NDP kinase / Nucleoside-2-P kinase


Mass: 15284.089 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halomonas (bacteria) / Strain: 593 / Gene: ndk / Plasmid: PET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q83WH5, nucleoside-diphosphate kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 5.02 Å3/Da / Density % sol: 75.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2M AMMONIUM ACETATE, 0.1M SODIUM CITRATE TRIBASIC DEHYDRATE, 30% PEG 4000, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Nov 12, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.3→77.08 Å / Num. obs: 25691 / % possible obs: 97.3 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 26
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.4 / % possible all: 92.1

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0070refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NHK

1nhk


Resolution: 2.3→35.35 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.898 / SU B: 7.235 / SU ML: 0.175 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.289 1303 5.1 %RANDOM
Rwork0.263 ---
obs0.265 25691 97.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.12 Å2
Baniso -1Baniso -2Baniso -3
1-1.72 Å20.86 Å20 Å2
2--1.72 Å20 Å2
3----2.59 Å2
Refinement stepCycle: LAST / Resolution: 2.3→35.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2128 0 0 57 2185
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222160
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1291.962914
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6715278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.58425104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.6515368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8891514
X-RAY DIFFRACTIONr_chiral_restr0.0750.2322
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211664
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6081.51390
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.14122214
X-RAY DIFFRACTIONr_scbond_it1.3973770
X-RAY DIFFRACTIONr_scangle_it2.5284.5700
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 79 -
Rwork0.336 1740 -
obs--92.01 %

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