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- PDB-1pae: nucleoside diphosphate kinase -

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Basic information

Entry
Database: PDB / ID: 1pae
Titlenucleoside diphosphate kinase
ComponentsNucleoside diphosphate kinase, cytosolic
KeywordsTRANSFERASE / selenocysteine selenomethionine
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 / negative regulation of pinocytosis / nucleoside triphosphate biosynthetic process / nucleoside-diphosphate kinase / UTP biosynthetic process ...dGTP biosynthetic process from dGDP / Azathioprine ADME / Ribavirin ADME / asexual reproduction / Interconversion of nucleotide di- and triphosphates / Neutrophil degranulation / negative regulation of pinocytosis / nucleoside triphosphate biosynthetic process / nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / nucleoside diphosphate kinase activity / negative regulation of exocytosis / GTP biosynthetic process / negative regulation of phagocytosis / translational elongation / phagocytic vesicle / secretory granule / response to bacterium / actin cytoskeleton organization / cytoskeleton / ribosome / G protein-coupled receptor signaling pathway / ATP binding / metal ion binding / plasma membrane / 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
SELENIUM ATOM / Nucleoside diphosphate kinase, cytosolic
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsStrub, M.-P. / Hoh, F. / Sanchez, J.-F. / Strub, J.M. / Bock, A. / Aumelas, A. / Dumas, C.
Citation
Journal: Structure / Year: 2003
Title: Selenomethionine and Selenocysteine Double Labeling Strategy for Crystallographic Phasing
Authors: Strub, M.-P. / Hoh, F. / Sanchez, J.-F. / Strub, J.M. / Bock, A. / Aumelas, A. / Dumas, C.
#1: Journal: Structure / Year: 2002
Title: Structure of the cathelicidin motif of protegrin-3 precursor: structural insights into the activation mechanism of an antimicrobial protein.
Authors: Sanchez, J.-F. / Hoh, F. / Strub, M.-P. / Aumelas, A. / Dumas, C.
History
DepositionMay 14, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 19, 2014Group: Atomic model / Structure summary
Revision 1.4Aug 6, 2014Group: Derived calculations / Structure summary
Revision 1.5Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 600HETEROGEN THE HETATM ENTRY SE 121 CORRESPONDS TO A SELENOCYSTEINE ADDUCT TO SEC 122 (NOT VISIBLE IN ...HETEROGEN THE HETATM ENTRY SE 121 CORRESPONDS TO A SELENOCYSTEINE ADDUCT TO SEC 122 (NOT VISIBLE IN THE ELECTRON DENSITY MAP EXCEPT SELENIUM ATOM) WITH A DISELENIDE BRIDGE BETWEEN SE 121 AND SE SEC X 122

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Nucleoside diphosphate kinase, cytosolic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1273
Polymers16,9691
Non-polymers1582
Water27015
1
X: Nucleoside diphosphate kinase, cytosolic
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)102,76118
Polymers101,8136
Non-polymers94812
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 area14810 Å2
ΔGint-115 kcal/mol
Surface area36410 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)76.633, 76.633, 106.510
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Nucleoside diphosphate kinase, cytosolic / NDK / NDP kinase


Mass: 16968.912 Da / Num. of mol.: 1 / Mutation: H122C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: ndk / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) selB::kan Cys51E / References: UniProt: P22887, nucleoside-diphosphate kinase
#2: Chemical ChemComp-SE / SELENIUM ATOM


Mass: 78.960 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Se
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.66 Å3/Da / Density % sol: 53.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 6000, magnesium chloride,Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
220 mMTris-HCl1dropp7.5
310 %(w/v)PEG60001reservoir
450 mMTris-HCl1reservoirpH7.5
510 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.9754 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 2003 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9754 Å / Relative weight: 1
ReflectionResolution: 2.7→24.71 Å / Num. all: 5418 / Num. obs: 5418 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 23 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 18.7
Reflection shellResolution: 2.7→2.77 Å / % possible all: 97.4
Reflection
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 25 Å / Num. measured all: 114811
Reflection shell
*PLUS
Lowest resolution: 2.74 Å / % possible obs: 97.4 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 3.1

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→24.71 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.927 / SU B: 10.98 / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.486 / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23216 595 11 %RANDOM
Rwork0.18215 ---
all0.1878 4823 --
obs0.18787 4823 98.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.258 Å2
Baniso -1Baniso -2Baniso -3
1-1.14 Å20.57 Å20 Å2
2--1.14 Å20 Å2
3----1.72 Å2
Refinement stepCycle: LAST / Resolution: 2.7→24.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1127 0 2 15 1144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221151
X-RAY DIFFRACTIONr_bond_other_d0.0020.021089
X-RAY DIFFRACTIONr_angle_refined_deg1.5441.9791555
X-RAY DIFFRACTIONr_angle_other_deg0.95832530
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4455147
X-RAY DIFFRACTIONr_chiral_restr0.1050.2175
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021275
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02232
X-RAY DIFFRACTIONr_nbd_refined0.1960.2205
X-RAY DIFFRACTIONr_nbd_other0.2260.21141
X-RAY DIFFRACTIONr_nbtor_other0.0940.2687
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.222
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0650.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2560.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0760.25
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.375 39
Rwork0.277 336
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 25 Å / Rfactor Rfree: 0.232 / Rfactor Rwork: 0.182
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.015
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.544

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