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- PDB-2nck: CRYSTAL STRUCTURE OF MYXOCOCCUS XANTHUS NUCLEOSIDE DIPHOSPHATE KI... -

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Basic information

Entry
Database: PDB / ID: 2nck
TitleCRYSTAL STRUCTURE OF MYXOCOCCUS XANTHUS NUCLEOSIDE DIPHOSPHATE KINASE AND ITS INTERACTION WITH A NUCLEOTIDE SUBSTRATE AT 2.0 ANGSTROMS RESOLUTION
ComponentsNUCLEOSIDE DIPHOSPHATE KINASENucleoside-diphosphate kinase
KeywordsPHOSPHOTRANSFERASE(PO4 AS ACCEPTOR)
Function / homology
Function and homology information


nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / phosphorylation / ATP binding / metal ion binding / 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
Nucleoside diphosphate kinase
Similarity search - Component
Biological speciesMyxococcus xanthus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsWilliams, R.L. / Oren, D.A. / Arnold, E.
Citation
Journal: J.Mol.Biol. / Year: 1993
Title: Crystal structure of Myxococcus xanthus nucleoside diphosphate kinase and its interaction with a nucleotide substrate at 2.0 A resolution.
Authors: Williams, R.L. / Oren, D.A. / Munoz-Dorado, J. / Inouye, S. / Inouye, M. / Arnold, E.
#1: Journal: J.Mol.Biol. / Year: 1991
Title: Crystallization and Preliminary X-Ray Diffraction Analysis of Nucleoside Diphosphate Kinase from Myxococcus Xanthus
Authors: Williams, R.L. / Munoz-Dorado, J. / Jacobo-Molina, A. / Inouye, S. / Inouye, M. / Arnold, E.
History
DepositionNov 15, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.5Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.6Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
R: NUCLEOSIDE DIPHOSPHATE KINASE
L: NUCLEOSIDE DIPHOSPHATE KINASE


Theoretical massNumber of molelcules
Total (without water)32,0512
Polymers32,0512
Non-polymers00
Water3,693205
1
R: NUCLEOSIDE DIPHOSPHATE KINASE
L: NUCLEOSIDE DIPHOSPHATE KINASE

R: NUCLEOSIDE DIPHOSPHATE KINASE
L: NUCLEOSIDE DIPHOSPHATE KINASE


Theoretical massNumber of molelcules
Total (without water)64,1024
Polymers64,1024
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)63.500, 63.500, 158.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.0047, -0.9876, 0.157), (-0.9887, -0.019, -0.1487), (0.14984, -0.156, -0.9763)
Vector: 66.701, 67.156, -0.39)

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Components

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


Mass: 16025.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myxococcus xanthus (bacteria) / References: UniProt: P15266, nucleoside-diphosphate kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.48 Å3/Da / Density % sol: 50.48 %
Crystal grow
*PLUS
pH: 5.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.3 Msodium acetate1drop
20.1 Macetic acid1drop
30.01 MEDTA1drop
413 %PEG33501drop
50.3 Msodium acetate1reservoir
60.1 Macetic acid1reservoir
716 %PEG33501reservoir
80.01 MEDTA1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 21862 / Rmerge(I) obs: 0.097

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.17 / Rfactor obs: 0.17 / Highest resolution: 2 Å
Refinement stepCycle: LAST / Highest resolution: 2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2247 0 0 205 2452
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.418
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
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 6 Å / Num. reflection obs: 20979 / Rfactor obs: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_d1.418
X-RAY DIFFRACTIONx_planar_d23.6
X-RAY DIFFRACTIONx_plane_restr0.0180.02
X-RAY DIFFRACTIONx_chiral_restr0.1350.12
X-RAY DIFFRACTIONx_mcbond_it1.311.5
X-RAY DIFFRACTIONx_scbond_it2.62.5
X-RAY DIFFRACTIONx_mcangle_it2.062
X-RAY DIFFRACTIONx_scangle_it3.96

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