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- PDB-3vgv: E134A mutant nucleoside diphosphate kinase derived from Halomonas... -

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Basic information

Entry
Database: PDB / ID: 3vgv
TitleE134A mutant 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: 2.5 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 21, 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 / 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

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Assembly

Deposited unit
A: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase
C: Nucleoside diphosphate kinase
D: Nucleoside diphosphate kinase
E: Nucleoside diphosphate kinase
F: Nucleoside diphosphate kinase
G: Nucleoside diphosphate kinase
H: Nucleoside diphosphate kinase
I: Nucleoside diphosphate kinase
J: Nucleoside diphosphate kinase
K: Nucleoside diphosphate kinase
L: Nucleoside diphosphate kinase
M: Nucleoside diphosphate kinase
N: Nucleoside diphosphate kinase
O: Nucleoside diphosphate kinase
P: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)243,61716
Polymers243,61716
Non-polymers00
Water3,747208
1
A: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)30,4522
Polymers30,4522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-12 kcal/mol
Surface area12080 Å2
MethodPISA
2
C: Nucleoside diphosphate kinase
D: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)30,4522
Polymers30,4522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-9 kcal/mol
Surface area12130 Å2
MethodPISA
3
E: Nucleoside diphosphate kinase
F: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)30,4522
Polymers30,4522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-10 kcal/mol
Surface area12350 Å2
MethodPISA
4
G: Nucleoside diphosphate kinase
H: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)30,4522
Polymers30,4522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-11 kcal/mol
Surface area12580 Å2
MethodPISA
5
I: Nucleoside diphosphate kinase
J: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)30,4522
Polymers30,4522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-12 kcal/mol
Surface area11800 Å2
MethodPISA
6
K: Nucleoside diphosphate kinase
L: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)30,4522
Polymers30,4522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-10 kcal/mol
Surface area12440 Å2
MethodPISA
7
M: Nucleoside diphosphate kinase
N: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)30,4522
Polymers30,4522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-9 kcal/mol
Surface area11470 Å2
MethodPISA
8
O: Nucleoside diphosphate kinase
P: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)30,4522
Polymers30,4522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-9 kcal/mol
Surface area12580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.165, 92.017, 113.613
Angle α, β, γ (deg.)90.00, 94.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 15226.054 Da / Num. of mol.: 16 / Mutation: E134A
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.: 208 / 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: 2.4 Å3/Da / Density % sol: 48.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2M CALCIUM ACETATE HYDRATE, 0.01M DITHIOTHREITOL (DTT), 0.1M SODIUM CACODYLATE TRIHYDRATE, 18% PEG 8000, 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: 2.5→42.95 Å / Num. obs: 73584 / % possible obs: 91.9 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.07
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 1.9 / % possible all: 82.2

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NHK

1nhk


Resolution: 2.5→42.95 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.868 / SU B: 12.258 / SU ML: 0.263 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.345 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.269 3697 5 %RANDOM
Rwork0.216 ---
obs0.218 73576 91.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å2-0.04 Å2
2--0.04 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.5→42.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16569 0 0 208 16777
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02216803
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.95822663
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.97552169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.5524.949792
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.499152845
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.28315108
X-RAY DIFFRACTIONr_chiral_restr0.0930.22528
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02112880
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_it0.9121.510874
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.72217288
X-RAY DIFFRACTIONr_scbond_it2.22835929
X-RAY DIFFRACTIONr_scangle_it3.8484.55375
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 260 -
Rwork0.336 4462 -
obs--80.32 %

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