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- PDB-1bux: 3'-PHOSPHORYLATED NUCLEOTIDES BINDING TO NUCLEOSIDE DIPHOSPHATE KINASE -

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Basic information

Entry
Database: PDB / ID: 1bux
Title3'-PHOSPHORYLATED NUCLEOTIDES BINDING TO NUCLEOSIDE DIPHOSPHATE KINASE
ComponentsNUCLEOSIDE DIPHOSPHATE KINASENucleoside-diphosphate kinase
KeywordsPHOSPHOTRANSFERASE / INHIBITOR / PAPS
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 / UTP 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 / UTP biosynthetic process / CTP 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-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
3'-PHOSPHATE-ADENOSINE-5'-PHOSPHATE SULFATE / Nucleoside diphosphate kinase, cytosolic
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsXu, Y. / Schneider, B. / Deville-Bonne, D. / Veron, M. / Janin, J.
Citation
Journal: J.Biol.Chem. / Year: 1998
Title: 3'-Phosphorylated nucleotides are tight binding inhibitors of nucleoside diphosphate kinase activity.
Authors: Schneider, B. / Xu, Y.W. / Janin, J. / Veron, M. / Deville-Bonne, D.
#1: Journal: Biochemistry / Year: 1995
Title: Mechanism of Phosphate Transfer by Nucleoside Diphosphate Kinase: X-Ray Structures of the Phosphohistidine Intermediate of the Enzymes from Drosophila and Dictyostelium
Authors: Morera, S. / Chiadmi, M. / Lebras, G. / Lascu, I. / Janin, J.
#2: Journal: Biochemistry / Year: 1994
Title: Adenosine 5'-Diphosphate Binding and the Active Site of Nucleoside Diphosphate Kinase
Authors: Morera, S. / Lascu, I. / Dumas, C. / Lebras, G. / Briozzo, P. / Veron, M. / Janin, J.
History
DepositionSep 7, 1998Processing site: BNL
Revision 1.0Apr 27, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NUCLEOSIDE DIPHOSPHATE KINASE
B: NUCLEOSIDE DIPHOSPHATE KINASE
C: NUCLEOSIDE DIPHOSPHATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9716
Polymers50,4493
Non-polymers1,5223
Water0
1
A: NUCLEOSIDE DIPHOSPHATE KINASE
B: NUCLEOSIDE DIPHOSPHATE KINASE
C: NUCLEOSIDE DIPHOSPHATE KINASE
hetero molecules

A: NUCLEOSIDE DIPHOSPHATE KINASE
B: NUCLEOSIDE DIPHOSPHATE KINASE
C: NUCLEOSIDE DIPHOSPHATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,94212
Polymers100,8986
Non-polymers3,0446
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+1/31
Unit cell
Length a, b, c (Å)71.500, 71.500, 153.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein NUCLEOSIDE DIPHOSPHATE KINASE / Nucleoside-diphosphate kinase / NDP KINASE


Mass: 16816.336 Da / Num. of mol.: 3
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: Chemical ChemComp-PPS / 3'-PHOSPHATE-ADENOSINE-5'-PHOSPHATE SULFATE / 3'-Phosphoadenosine-5'-phosphosulfate


Mass: 507.264 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O13P2S

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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: 2.25 Å3/Da / Density % sol: 38 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal
*PLUS
Crystal grow
*PLUS
pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
130-32 %PEG5501reservoir
250 mMTris-HCl1reservoir
320 mM1reservoirMgCl2
45 mg/mlprotein1drop
515-16 %PEG5501drop
650 mMTris-HCl1drop
720 mM1dropMgCl2
817 mM3'-amino-ADP1drop

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Apr 1, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→15 Å / Num. obs: 10703 / % possible obs: 91.5 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 58.5 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 18
Reflection shellResolution: 2.8→2.9 Å / Mean I/σ(I) obs: 3.3 / Rsym value: 0.338 / % possible all: 95.7

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→10 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.312 -10 %RANDOM
Rwork0.204 ---
obs0.204 10268 89.5 %-
Displacement parametersBiso mean: 31.6 Å2
Refine analyzeLuzzati d res low obs: 4.5 Å / Luzzati sigma a obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3441 0 85 0 3526
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.53
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.53

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