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- PDB-1wkj: Crystal Structure of Nucleoside Diphosphate Kinase from Thermus t... -

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Basic information

Entry
Database: PDB / ID: 1wkj
TitleCrystal Structure of Nucleoside Diphosphate Kinase from Thermus thermophilus HB8
Componentsnucleoside diphosphate kinase
KeywordsTRANSFERASE / nucleoside diphosphate kinase / Thermus thermophilus HB8 / kinase / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
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 / 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 speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTakeishi, S. / Nakagawa, N. / Masui, R. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure of Nucleoside Diphosphate Kinase from Thermus thermophilus HB8
Authors: Takeishi, S. / Nakagawa, N. / Masui, R. / Kuramitsu, S.
History
DepositionMay 31, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 23, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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)30,7342
Polymers30,7342
Non-polymers00
Water3,243180
1
A: nucleoside diphosphate kinase
B: nucleoside diphosphate kinase

A: nucleoside diphosphate kinase
B: nucleoside diphosphate kinase

A: nucleoside diphosphate kinase
B: nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)92,2016
Polymers92,2016
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Unit cell
Length a, b, c (Å)123.676, 123.676, 104.527
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
DetailsThe biological assembly is a hexamer generated from the dimer in the asymmetric unit by the operations: -y+1, x-y+1, z and -x+y, -x+1, z.

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Components

#1: Protein nucleoside diphosphate kinase


Mass: 15366.903 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: ndk / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SLV5, nucleoside-diphosphate kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 3.8 Å3/Da / Density % sol: 67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 10% PEG4000, 0.09M Ammonium Acetate, 15% Glycerol, 0.1M Sodium Citrate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 0.98 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Apr 11, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 387285 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 12 % / Biso Wilson estimate: 27.8 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 39
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.274 / Mean I/σ(I) obs: 12.7 / % possible all: 100

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HHQ

1hhq


Resolution: 2→50 Å / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.238 3115 -RANDOM
Rwork0.208 ---
all-32217 --
obs-31293 96.6 %-
Displacement parametersBiso mean: 29.3 Å2
Baniso -1Baniso -2Baniso -3
1--2.021 Å2-1.045 Å20 Å2
2---2.021 Å20 Å2
3---4.042 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2158 0 0 180 2338
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2

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