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- PDB-1nsk: THE CRYSTAL STRUCTURE OF A HUMAN NUCLEOSIDE DIPHOSPHATE KINASE, N... -

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Basic information

Entry
Database: PDB / ID: 1nsk
TitleTHE CRYSTAL STRUCTURE OF A HUMAN NUCLEOSIDE DIPHOSPHATE KINASE, NM23-H2
ComponentsNUCLEOSIDE DIPHOSPHATE KINASE
KeywordsPHOSPHOTRANSFERASE (PO4 AS ACCEPTOR)
Function / homology
Function and homology information


regulation of epidermis development / nucleoside triphosphate biosynthetic process / protein histidine kinase activity / Ribavirin ADME / G-quadruplex DNA binding / nucleoside-diphosphate kinase / positive regulation of keratinocyte differentiation / Interconversion of nucleotide di- and triphosphates / UTP biosynthetic process / CTP biosynthetic process ...regulation of epidermis development / nucleoside triphosphate biosynthetic process / protein histidine kinase activity / Ribavirin ADME / G-quadruplex DNA binding / nucleoside-diphosphate kinase / positive regulation of keratinocyte differentiation / Interconversion of nucleotide di- and triphosphates / UTP biosynthetic process / CTP biosynthetic process / Azathioprine ADME / nucleoside diphosphate kinase activity / GTP biosynthetic process / histidine kinase / ruffle / positive regulation of epithelial cell proliferation / integrin-mediated signaling pathway / cell periphery / GDP binding / lamellipodium / secretory granule lumen / regulation of apoptotic process / ficolin-1-rich granule lumen / transcription coactivator activity / cell adhesion / Neutrophil degranulation / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / positive regulation of transcription by RNA polymerase II / DNA binding / extracellular exosome / extracellular region / ATP binding / metal ion binding / identical protein binding / nucleus / cytoplasm / cytosol
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 (NDPK)-like domain profile. / 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, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase (NDPK)-like domain profile. / 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 B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsWilliams, R.L. / Perisic, O.
CitationJournal: J.Mol.Biol. / Year: 1995
Title: The crystal structure of a human nucleoside diphosphate kinase, NM23-H2.
Authors: Webb, P.A. / Perisic, O. / Mendola, C.E. / Backer, J.M. / Williams, R.L.
History
DepositionJul 4, 1995Processing site: BNL
Revision 1.0Oct 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
R: NUCLEOSIDE DIPHOSPHATE KINASE
L: NUCLEOSIDE DIPHOSPHATE KINASE
T: NUCLEOSIDE DIPHOSPHATE KINASE
U: NUCLEOSIDE DIPHOSPHATE KINASE
N: NUCLEOSIDE DIPHOSPHATE KINASE
O: NUCLEOSIDE DIPHOSPHATE KINASE


Theoretical massNumber of molelcules
Total (without water)103,9446
Polymers103,9446
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15450 Å2
ΔGint-97 kcal/mol
Surface area36880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.670, 118.800, 90.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.011722, -0.99971, 0.020906), (-0.999911, -0.011854, -0.006192), (0.006438, -0.020832, -0.999762)87.6304, 89.5592, 67.9659
2given(0.028594, 0.01165, -0.999523), (0.009486, -0.99989, -0.011383), (-0.999546, -0.009156, -0.028701)79.3793, 82.5227, 82.549
3given(-0.999838, 0.015465, -0.009183), (0.009302, 0.007614, -0.999928), (-0.015394, -0.999851, -0.007757)94.8163, 74.361, 76.0753
4given(-0.026048, 0.99966, 0.001129), (-0.026962, -0.001832, 0.999635), (0.999297, 0.026008, 0.027)7.3653, 8.9439, -15.8543
5given(-0.015557, -0.026262, 0.999534), (0.999875, -0.003176, 0.015479), (0.002768, 0.99965, 0.026309)15.6332, -6.6, -8.6207

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Components

#1: Protein
NUCLEOSIDE DIPHOSPHATE KINASE


Mass: 17324.055 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NM23-H2 / Plasmid: PMAL-C2 (NEW ENGLAND BIOLABS) / Gene (production host): NM23-H2 / Production host: Escherichia coli (E. coli) / References: UniProt: P22392, nucleoside-diphosphate kinase

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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: 3.06 Å3/Da / Density % sol: 59.76 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 MTris-HCl1drop
21.8 Mammonium sulfate1drop
315 %(w/v)glycerol1drop
40.1 MTris-HCl1reservoir
52.2 Mammonium sulfate1reservoir
620 %(w/v)glycerol1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→25 Å / Num. obs: 29553 / % possible obs: 92.8 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.087
Reflection
*PLUS
Rmerge(I) obs: 0.087

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MOSFLMdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.8→6 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.294 -2.85 %
Rwork0.249 --
obs0.249 26512 89.8 %
Displacement parametersBiso mean: 29.63 Å2
Refinement stepCycle: LAST / Resolution: 2.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7206 0 0 0 7206
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
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_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

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