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- PDB-1jxv: Crystal Structure of Human Nucleoside Diphosphate Kinase A -

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Basic information

Entry
Database: PDB / ID: 1jxv
TitleCrystal Structure of Human Nucleoside Diphosphate Kinase A
ComponentsNucleoside Diphosphate Kinase A
KeywordsTRANSFERASE / kinase
Function / homology
Function and homology information


DNA nuclease activity / Ribavirin ADME / nucleoside-diphosphate kinase / Interconversion of nucleotide di- and triphosphates / UTP biosynthetic process / CTP biosynthetic process / Azathioprine ADME / nucleoside diphosphate kinase activity / positive regulation of DNA binding / GTP biosynthetic process ...DNA nuclease activity / Ribavirin ADME / nucleoside-diphosphate kinase / Interconversion of nucleotide di- and triphosphates / UTP biosynthetic process / CTP biosynthetic process / Azathioprine ADME / nucleoside diphosphate kinase activity / positive regulation of DNA binding / GTP biosynthetic process / ribosomal small subunit binding / lactation / 3'-5' exonuclease activity / positive regulation of epithelial cell proliferation / ruffle membrane / endocytosis / nervous system development / regulation of apoptotic process / cell differentiation / early endosome / negative regulation of cell population proliferation / GTP binding / magnesium ion binding / RNA binding / extracellular exosome / ATP binding / identical protein binding / nucleus / membrane / cytosol / cytoplasm
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 A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMin, K. / Song, H.K. / Chang, C. / Kim, S.Y. / Lee, K.J. / Suh, S.W.
Citation
Journal: Proteins / Year: 2002
Title: Crystal structure of human nucleoside diphosphate kinase A, a metastasis suppressor.
Authors: Min, K. / Song, H.K. / Chang, C. / Kim, S.Y. / Lee, K.J. / Suh, S.W.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization and preliminary X-ray crystallographic analysis of human nucleoside diphosphate kinase A
Authors: Min, K. / Kim, S.Y. / Song, H.K. / Chang, C. / Cho, S.J. / Moon, J. / Yang, J.K. / Lee, J.Y. / Lee, K.J. / Suh, S.W.
History
DepositionSep 10, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 10, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoside Diphosphate Kinase A
B: Nucleoside Diphosphate Kinase A
C: Nucleoside Diphosphate Kinase A
D: Nucleoside Diphosphate Kinase A
E: Nucleoside Diphosphate Kinase A
F: Nucleoside Diphosphate Kinase A


Theoretical massNumber of molelcules
Total (without water)103,0246
Polymers103,0246
Non-polymers00
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16030 Å2
ΔGint-92 kcal/mol
Surface area33420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.21, 78.11, 82.29
Angle α, β, γ (deg.)90, 101.33, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Nucleoside Diphosphate Kinase A


Mass: 17170.721 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: nm23-H1 / Plasmid: pET-3c / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P15531, nucleoside-diphosphate kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.27 Å3/Da / Density % sol: 45.81 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.35
Details: MPD, MES-KOH, pH 6.35, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 288 K
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
117 mg/mlprotein1drop
2100 mMMES/KOH1reservoir
330-34 %(v/v)MPD1reservoirpH6.35

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 48679 / % possible obs: 90.9 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.1
Reflection
*PLUS
Lowest resolution: 50 Å

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLORrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NUE

1nue


Resolution: 2.2→6 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.263 1890 5.366 %
Rwork0.207 --
all-37113 -
obs-35223 -
Refinement stepCycle: LAST / Resolution: 2.2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7104 0 0 191 7295
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1
X-RAY DIFFRACTIONx_bond_d0.009
Refinement
*PLUS
σ(F): 2 / Rfactor obs: 0.207
Solvent computation
*PLUS
Displacement parameters
*PLUS

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