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- PDB-1b99: 3'-FLUORO-URIDINE DIPHOSPHATE BINDING TO NUCLEOSIDE DIPHOSPHATE KINASE -

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Basic information

Entry
Database: PDB / ID: 1b99
Title3'-FLUORO-URIDINE DIPHOSPHATE BINDING TO NUCLEOSIDE DIPHOSPHATE KINASE
ComponentsPROTEIN (NUCLEOSIDE DIPHOSPHATE KINASE)
KeywordsTRANSFERASE / PHOSPHOTRANSFERASE / ANTIVIRAL AGENT / FLUOROURIDINE
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 / negative regulation of exocytosis / GTP biosynthetic process / negative regulation of phagocytosis / nucleoside diphosphate kinase activity / 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 (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
2',3'-DIDEOXY-3'-FLUORO-URIDIDINE-5'-DIPHOSPHATE / PYROPHOSPHATE 2- / Nucleoside diphosphate kinase, cytosolic
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsJanin, J. / Xu, Y.
Citation
Journal: Biochemistry / Year: 1999
Title: Catalytic mechanism of nucleoside diphosphate kinase investigated using nucleotide analogues, viscosity effects, and X-ray crystallography.
Authors: Gonin, P. / Xu, Y. / Milon, L. / Dabernat, S. / Morr, M. / Kumar, R. / Lacombe, M.L. / Janin, J. / Lascu, I.
#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
DepositionFeb 22, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Jun 28, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: PROTEIN (NUCLEOSIDE DIPHOSPHATE KINASE)
B: PROTEIN (NUCLEOSIDE DIPHOSPHATE KINASE)
C: PROTEIN (NUCLEOSIDE DIPHOSPHATE KINASE)
D: PROTEIN (NUCLEOSIDE DIPHOSPHATE KINASE)
E: PROTEIN (NUCLEOSIDE DIPHOSPHATE KINASE)
F: PROTEIN (NUCLEOSIDE DIPHOSPHATE KINASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,16812
Polymers100,8986
Non-polymers1,2706
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14890 Å2
ΔGint-46 kcal/mol
Surface area34740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.020, 105.310, 70.350
Angle α, β, γ (deg.)90.00, 117.43, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: Protein
PROTEIN (NUCLEOSIDE DIPHOSPHATE KINASE) / E.C.2.7.4.6 / NDPK


Mass: 16816.336 Da / Num. of mol.: 6 / Fragment: HEXAMER
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-FUP / 2',3'-DIDEOXY-3'-FLUORO-URIDIDINE-5'-DIPHOSPHATE / FUDP


Mass: 390.153 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13FN2O10P2
#3: Chemical
ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: H2O7P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.28 Å3/Da / Density % sol: 46.06 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5 / Details: pH 7.5, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 600011
2tris11
3MGCL211
4NDPK11
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
215 mMnucleotide1reservoir
350 mMTris-HCl1reservoir
420 mM1reservoirMgCl2
516 %PEG60001reservoir

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Data collection

DiffractionMean temperature: 278 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jan 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→10 Å / Num. obs: 19653 / % possible obs: 81 % / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Rmerge(I) obs: 0.092
Reflection
*PLUS
Num. obs: 19650

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Processing

Software
NameClassification
AMoREphasing
X-PLORrefinement
MOSFLMdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LWX

1lwx


Resolution: 2.7→6 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.304 -7 %RANDOM
Rwork0.207 ---
obs-19650 81 %-
Displacement parametersBiso mean: 23.5 Å2
Refinement stepCycle: LAST / Resolution: 2.7→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6882 0 69 19 6970
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.5
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_d1.25
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_deg1.25

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