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- PDB-1b4s: STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE H122G MUTANT -

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Basic information

Entry
Database: PDB / ID: 1b4s
TitleSTRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE H122G MUTANT
ComponentsNUCLEOSIDE DIPHOSPHATE KINASENucleoside-diphosphate kinase
KeywordsPHOSPHOTRANSFERASE / TRANSFERASE / KINASE / ATP-BINDING
Function / homologyNucleoside diphosphate kinase / Nucleoside diphosphate kinases active site. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase-like domain superfamily / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase, active site / dGTP biosynthetic process from dGDP / dGDP phosphorylation / asexual reproduction / negative regulation of pinocytosis ...Nucleoside diphosphate kinase / Nucleoside diphosphate kinases active site. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase-like domain superfamily / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase, active site / dGTP biosynthetic process from dGDP / dGDP phosphorylation / asexual reproduction / negative regulation of pinocytosis / nucleoside triphosphate biosynthetic process / negative regulation of exocytosis / negative regulation of phagocytosis / nucleoside-diphosphate kinase / CTP biosynthetic process / UTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / translational elongation / phagocytic vesicle / secretory granule / response to bacterium / actin cytoskeleton organization / ribosome / cytoskeleton / G protein-coupled receptor signaling pathway / ATP binding / plasma membrane / metal ion binding / cytoplasm / Nucleoside diphosphate kinase, cytosolic
Function and homology information
Specimen sourceDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 2.5 Å resolution
AuthorsMeyer, P. / Janin, J.
Citation
Journal: Biochemistry / Year: 1999
Title: Nucleophilic activation by positioning in phosphoryl transfer catalyzed by nucleoside diphosphate kinase.
Authors: Admiraal, S.J. / Schneider, B. / Meyer, P. / Janin, J. / Veron, M. / Deville-Bonne, D. / Herschlag, 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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 28, 1998 / Release: Jun 15, 1999
RevisionDateData content typeGroupProviderType
1.0Jun 15, 1999Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,84512
Polyers50,2063
Non-polymers1,6399
Water1,946108
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)103,69024
Polyers100,4116
Non-polymers3,27918
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+1/31
Unit cell
γ
α
β
Length a, b, c (Å)70.000, 70.000, 151.770
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP 31 2 1

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Components

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


Mass: 16735.242 Da / Num. of mol.: 3 / Mutation: H122G / Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Genus: Dictyostelium / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / References: UniProt: P22887, nucleoside-diphosphate kinase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Formula: PO4 / Phosphate
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Formula: Mg / Magnesium
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Formula: H2O / Water

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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: 2.14 / Density percent sol: 42.44 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Temp: 18 ℃ / Method: vapor diffusion, hanging drop
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
121 %PEG4001drop
220 mM1dropMgCl2
3100 mMTris-HCl1drop
410 mMATP1drop
542 %PEG4001reservoir

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Type: LURE BEAMLINE D41A / Synchrotron site: LURE / Beamline: D41A / Wavelength: 1.375
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Collection date: Jul 1, 1998
RadiationMonochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.375 Å / Relative weight: 1
ReflectionD resolution high: 2.5 Å / D resolution low: 8 Å / Number obs: 14555 / Observed criterion sigma I: 3 / Rmerge I obs: 0.083 / Redundancy: 9.8 % / Percent possible obs: 99.9
Reflection
*PLUS
Number obs: 15492 / Number measured all: 150824
Reflection shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.59 Å / Rmerge I obs: 0.3

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KDN
Details: MUTANT HAS LOST NDPK ACTIVITY, BUT EFFICIENTLY PHOSPHORYLATES IMIDAZOLE AND OTHER PHOSPHATE ACCEPTOR MOLECULES (AMINES AND ALCOHOLS). THE PROTEIN WAS CRYSTALLIZED WITH ATP, BUT THE NUCLEOTIDE IS SEEN TO BE HYDROLYZED TO ADP+PO4 IN THE CRYSTAL.
R Free selection details: RANDOM / Sigma F: 2
Displacement parametersB iso mean: 22 Å2
Least-squares processR factor R free: 0.305 / R factor R work: 0.203 / R factor obs: 0.203 / Highest resolution: 2.5 Å / Lowest resolution: 8 Å / Number reflection obs: 14555 / Percent reflection obs: 99.9
Refine hist #LASTHighest resolution: 2.5 Å / Lowest resolution: 8 Å
Number of atoms included #LASTProtein: 3423 / Nucleic acid: 99 / Ligand: 3 / Solvent: 108 / Total: 3633
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.9
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_d2.0
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
Least-squares process
*PLUS
Percent reflection R free: 7.5
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.0

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