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- PDB-1hlw: STRUCTURE OF THE H122A MUTANT OF THE NUCLEOSIDE DIPHOSPHATE KINASE -

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Basic information

Entry
Database: PDB / ID: 1hlw
TitleSTRUCTURE OF THE H122A MUTANT OF THE NUCLEOSIDE DIPHOSPHATE KINASE
ComponentsNUCLEOSIDE DIPHOSPHATE KINASE
KeywordsTRANSFERASE / PHOSPHOTRANSFERASE / KINASE / ATP-BINDING
Function / homology
Function and homology information


dGTP biosynthetic process from dGDP / Azathioprine ADME / Ribavirin ADME / asexual reproduction / Interconversion of nucleotide di- and triphosphates / Neutrophil degranulation / nucleoside triphosphate biosynthetic process / negative regulation of pinocytosis / nucleoside-diphosphate kinase / CTP biosynthetic process ...dGTP biosynthetic process from dGDP / Azathioprine ADME / Ribavirin ADME / asexual reproduction / Interconversion of nucleotide di- and triphosphates / Neutrophil degranulation / nucleoside triphosphate biosynthetic process / negative regulation of pinocytosis / nucleoside-diphosphate kinase / CTP biosynthetic process / UTP biosynthetic process / negative regulation of exocytosis / negative regulation of phagocytosis / GTP biosynthetic process / nucleoside diphosphate kinase activity / translational elongation / phagocytic vesicle / secretory granule / response to bacterium / actin cytoskeleton organization / cytoskeleton / ribosome / G protein-coupled receptor signaling pathway / phosphorylation / ATP binding / metal ion 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, cytosolic
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsAdmiraal, S.J. / Meyer, P. / Schneider, B. / Deville-Bonne, D. / Janin, J. / Herschlag, D.
CitationJournal: Biochemistry / Year: 2001
Title: Chemical rescue of phosphoryl transfer in a cavity mutant: a cautionary tale for site-directed mutagenesis.
Authors: Admiraal, S.J. / Meyer, P. / Schneider, B. / Deville-Bonne, D. / Janin, J. / Herschlag, D.
History
DepositionDec 4, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NUCLEOSIDE DIPHOSPHATE KINASE


Theoretical massNumber of molelcules
Total (without water)16,7491
Polymers16,7491
Non-polymers00
Water2,270126
1
A: NUCLEOSIDE DIPHOSPHATE KINASE
x 6


Theoretical massNumber of molelcules
Total (without water)100,4966
Polymers100,4966
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
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_555-x+y,y,-z+1/21
crystal symmetry operation12_565x,x-y+1,-z+1/21
Buried area12810 Å2
ΔGint-62 kcal/mol
Surface area36090 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)75.001, 75.001, 106.169
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
DetailsThe biological assembly is a homohexamer

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Components

#1: Protein NUCLEOSIDE DIPHOSPHATE KINASE


Mass: 16749.268 Da / Num. of mol.: 1 / Mutation: H122A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: P22887, nucleoside-diphosphate kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.57 Å3/Da / Density % sol: 52.17 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 600, Magnesium Chloride, Tris Hydrochloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 %PEG6001drop
220 mM1dropMgCl2
350 mMTris-HCl1drop
412.5 mg/mlprotein1drop
520 %PEG6001reservoir
620 mM1reservoirMgCl2
750 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 110350 / Num. obs: 13910 / % possible obs: 95.8 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.069
Reflection shellResolution: 1.9→2.02 Å / % possible all: 88
Reflection
*PLUS
Num. measured all: 110350

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.9→30 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2300066.55 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.208 1137 8.2 %RANDOM
Rwork0.166 ---
obs0.166 13909 95.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.57 Å2 / ksol: 0.319 e/Å3
Displacement parametersBiso mean: 28.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.76 Å22.69 Å20 Å2
2--0.76 Å20 Å2
3----1.53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1142 0 0 126 1268
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.16
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.911.5
X-RAY DIFFRACTIONc_mcangle_it3.742
X-RAY DIFFRACTIONc_scbond_it5.892
X-RAY DIFFRACTIONc_scangle_it7.932.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.25 198 9.5 %
Rwork0.214 1876 -
obs--88 %
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 8.2 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 28.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.16
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.25 / % reflection Rfree: 9.5 % / Rfactor Rwork: 0.214

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