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- PDB-1nsq: MECHANISM OF PHOSPHATE TRANSFER BY NUCLEOSIDE DIPHOSPHATE KINASE:... -

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Entry
Database: PDB / ID: 1nsq
TitleMECHANISM OF PHOSPHATE TRANSFER BY NUCLEOSIDE DIPHOSPHATE KINASE: X-RAY STRUCTURES OF A PHOSPHO-HISTIDINE INTERMEDIATE OF THE ENZYMES FROM DROSOPHILA AND DICTYOSTELIUM
ComponentsNUCLEOSIDE DIPHOSPHATE KINASE
KeywordsPHOSPHOTRANSFERASE
Function / homology
Function and homology information


ribonucleoside triphosphate biosynthetic process / regulation of tube architecture, open tracheal system / Azathioprine ADME / Ribavirin ADME / establishment or maintenance of polarity of follicular epithelium / open tracheal system development / epithelial cell migration, open tracheal system / Interconversion of nucleotide di- and triphosphates / deoxyribonucleoside triphosphate biosynthetic process / nuclear microtubule ...ribonucleoside triphosphate biosynthetic process / regulation of tube architecture, open tracheal system / Azathioprine ADME / Ribavirin ADME / establishment or maintenance of polarity of follicular epithelium / open tracheal system development / epithelial cell migration, open tracheal system / Interconversion of nucleotide di- and triphosphates / deoxyribonucleoside triphosphate biosynthetic process / nuclear microtubule / Neutrophil degranulation / nucleoside-diphosphate kinase / nucleotide metabolic process / adherens junction organization / UTP biosynthetic process / CTP biosynthetic process / nucleoside diphosphate kinase activity / GTP biosynthetic process / microtubule-based process / kinase activity / mitotic cell cycle / microtubule binding / microtubule / GTP binding / magnesium ion binding / mitochondrion / ATP binding / plasma membrane
Similarity search - Function
Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase (NDPK)-like domain profile. / 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-like domain / Nucleoside diphosphate kinase (NDPK)-like domain profile. / 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
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / Resolution: 2.18 Å
AuthorsJanin, J. / Chiadmi, M. / Morera, S. / Lebras, G. / Lascu, I.
Citation
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.
#1: Journal: Structure / Year: 1993
Title: Crystal Structure of the Awd Nucleoside Diphosphate Kinase from Drosophila
Authors: Chiadmi, M. / Morera, S. / Lascu, I. / Dumas, C. / Lebras, G. / Veron, M. / Janin, J.
#2: Journal: Embo J. / Year: 1992
Title: X-Ray Structure of Nucleoside Diphosphate Kinase
Authors: Dumas, C. / Lascu, I. / Morera, S. / Glaser, P. / Fourme, R. / Wallet, V. / Lacombe, M.L. / Veron, M. / Janin, J.
History
DepositionApr 24, 1995Processing site: BNL
Revision 1.0Jul 10, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jun 5, 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_conn
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_conn.pdbx_leaving_atom_flag

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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
C: NUCLEOSIDE DIPHOSPHATE KINASE


Theoretical massNumber of molelcules
Total (without water)51,8123
Polymers51,8123
Non-polymers00
Water4,630257
1
A: NUCLEOSIDE DIPHOSPHATE KINASE
B: NUCLEOSIDE DIPHOSPHATE KINASE
C: NUCLEOSIDE DIPHOSPHATE KINASE

A: NUCLEOSIDE DIPHOSPHATE KINASE
B: NUCLEOSIDE DIPHOSPHATE KINASE
C: NUCLEOSIDE DIPHOSPHATE KINASE


Theoretical massNumber of molelcules
Total (without water)103,6256
Polymers103,6256
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_766-x+2,-x+y+1,-z+5/31
Buried area16800 Å2
ΔGint-82 kcal/mol
Surface area35430 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)115.750, 115.750, 98.520
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein NUCLEOSIDE DIPHOSPHATE KINASE


Mass: 17270.830 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / References: UniProt: P08879, nucleoside-diphosphate kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.68 Å3/Da / Density % sol: 66.53 %
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 %PEG60001drop
220 mM1dropMgCl2
350 mMTris-HCl1drop
410 %PEG60001reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.17→15.1 Å / Num. obs: 32198 / % possible obs: 79 %
Reflection
*PLUS
Num. measured all: 184822 / Rmerge(I) obs: 0.077

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.18→8 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.18 -
obs0.18 30950
Refinement stepCycle: LAST / Resolution: 2.18→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3621 0 0 257 3878
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_deg1.59
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_d
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
Refinement
*PLUS
Num. reflection obs: 31522
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 22 Å2

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