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- PDB-7ztk: NME1 in complex with CoA -

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Basic information

Entry
Database: PDB / ID: 7ztk
TitleNME1 in complex with CoA
ComponentsNucleoside diphosphate kinase A
KeywordsTRANSFERASE / NME1 / complex / nucleoside diphosphate kinase 1 / coenzyme-A
Function / homology
Function and homology information


intermediate filament binding / negative regulation of myeloid leukocyte differentiation / Azathioprine ADME / Ribavirin ADME / Interconversion of nucleotide di- and triphosphates / DNA nuclease activity / mammary gland development / nucleoside-diphosphate kinase / gamma-tubulin binding / UTP biosynthetic process ...intermediate filament binding / negative regulation of myeloid leukocyte differentiation / Azathioprine ADME / Ribavirin ADME / Interconversion of nucleotide di- and triphosphates / DNA nuclease activity / mammary gland development / nucleoside-diphosphate kinase / gamma-tubulin binding / UTP biosynthetic process / CTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / dTMP biosynthetic process / ribosomal small subunit binding / lactation / 3'-5' exonuclease activity / positive regulation of epithelial cell proliferation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / positive regulation of neuron projection development / ruffle membrane / endocytosis / myelin sheath / single-stranded DNA binding / nervous system development / mitochondrial outer membrane / cell differentiation / early endosome / negative regulation of gene expression / centrosome / GTP binding / protein kinase binding / perinuclear region of cytoplasm / enzyme binding / magnesium ion binding / mitochondrion / ATP binding / identical protein binding / nucleus / cytosol
Similarity search - Function
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
Similarity search - Domain/homology
COENZYME A / Nucleoside diphosphate kinase A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGarcia-Saez, I. / Iuso, D. / Khochbin, S. / Petosa, C.
Funding support France, 1items
OrganizationGrant numberCountry
Other government France
CitationJournal: Sci Adv / Year: 2023
Title: Nucleoside diphosphate kinases 1 and 2 regulate a protective liver response to a high-fat diet.
Authors: Iuso, D. / Garcia-Saez, I. / Coute, Y. / Yamaryo-Botte, Y. / Boeri Erba, E. / Adrait, A. / Zeaiter, N. / Tokarska-Schlattner, M. / Jilkova, Z.M. / Boussouar, F. / Barral, S. / Signor, L. / ...Authors: Iuso, D. / Garcia-Saez, I. / Coute, Y. / Yamaryo-Botte, Y. / Boeri Erba, E. / Adrait, A. / Zeaiter, N. / Tokarska-Schlattner, M. / Jilkova, Z.M. / Boussouar, F. / Barral, S. / Signor, L. / Couturier, K. / Hajmirza, A. / Chuffart, F. / Bourova-Flin, E. / Vitte, A.L. / Bargier, L. / Puthier, D. / Decaens, T. / Rousseaux, S. / Botte, C. / Schlattner, U. / Petosa, C. / Khochbin, S.
History
DepositionMay 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,97212
Polymers105,3676
Non-polymers4,6056
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, mass spectrometry, native mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21750 Å2
ΔGint-121 kcal/mol
Surface area34300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.173, 69.450, 116.296
Angle α, β, γ (deg.)90.000, 90.060, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Nucleoside diphosphate kinase A / NDK A / NDP kinase A / Metastasis inhibition factor NM23 / NDPK-A / Tumor metastatic process- ...NDK A / NDP kinase A / Metastasis inhibition factor NM23 / NDPK-A / Tumor metastatic process-associated protein / nm23-M1


Mass: 17561.199 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: NME1 hexamer in complex with CoA / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nme1, Nm23 / Plasmid: pETM-11
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P15532, nucleoside-diphosphate kinase
#2: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.08 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 36% PEG 3350, 0.2M Mg(NO3)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.6→49.13 Å / Num. obs: 26764 / % possible obs: 99.23 % / Redundancy: 3.2 % / Biso Wilson estimate: 40.72 Å2 / CC1/2: 0.945 / CC star: 0.986 / Rmerge(I) obs: 0.254 / Rpim(I) all: 0.17 / Rrim(I) all: 0.307 / Net I/σ(I): 3.37
Reflection shellResolution: 2.6→2.693 Å / Redundancy: 3.3 % / Rmerge(I) obs: 1.046 / Mean I/σ(I) obs: 0.84 / Num. unique obs: 2649 / CC1/2: 0.542 / CC star: 0.839 / Rpim(I) all: 0.684 / Rrim(I) all: 1.253 / % possible all: 98.53

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ui4

5ui4


Resolution: 2.6→49.13 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.35 / Stereochemistry target values: ML
Details: TLS was used in the first runs of refinement (1 group/chain), but not in the last runs of refinement.
RfactorNum. reflection% reflection
Rfree0.2893 1322 4.97 %
Rwork0.2725 25271 -
obs0.2733 26593 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.33 Å2 / Biso mean: 47.6645 Å2 / Biso min: 18.25 Å2
Refinement stepCycle: final / Resolution: 2.6→49.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7266 0 254 77 7597
Biso mean--70.9 41.05 -
Num. residues----912
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.70.37111090.38772821293098
2.7-2.830.36381500.30862732288299
2.83-2.980.31461470.29832782292999
2.98-3.160.31381570.30162797295499
3.16-3.410.31971710.28182770294199
3.41-3.750.29971800.269127542934100
3.75-4.290.25671440.25728512995100
4.29-5.410.24481280.243728602988100
5.41-49.130.26911360.247229043040100

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