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- PDB-7zlw: NME1 in complex with ADP -

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Basic information

Entry
Database: PDB / ID: 7zlw
TitleNME1 in complex with ADP
ComponentsNucleoside diphosphate kinase A
KeywordsTRANSFERASE / NME1 / complex / nucleoside diphosphate kinase 1 / ADP
Function / homology
Function and homology information


Azathioprine ADME / Ribavirin ADME / Interconversion of nucleotide di- and triphosphates / DNA nuclease activity / nucleoside-diphosphate kinase / mammary gland development / UTP biosynthetic process / CTP biosynthetic process / dTMP biosynthetic process / nucleoside diphosphate kinase activity ...Azathioprine ADME / Ribavirin ADME / Interconversion of nucleotide di- and triphosphates / DNA nuclease activity / nucleoside-diphosphate kinase / mammary gland development / UTP biosynthetic process / CTP biosynthetic process / dTMP biosynthetic process / nucleoside diphosphate kinase activity / GTP biosynthetic process / ribosomal small subunit binding / lactation / 3'-5' exonuclease activity / positive regulation of epithelial cell proliferation / ruffle membrane / endocytosis / nervous system development / myelin sheath / cell differentiation / early endosome / GTP binding / magnesium ion binding / mitochondrion / ATP binding / identical protein binding / nucleus / cytosol
Similarity search - Function
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
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Nucleoside diphosphate kinase A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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
DepositionApr 15, 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
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,50311
Polymers105,3676
Non-polymers2,1365
Water8,143452
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 area19470 Å2
ΔGint-110 kcal/mol
Surface area34600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.656, 70.193, 113.167
Angle α, β, γ (deg.)90.000, 90.960, 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: The chain E of hexameric NME1 does not have ADP bound. Some residues around the nucleotide binding region are disordered.
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-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 452 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 1.99 Å3/Da / Density % sol: 38.05 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG 400, NaCl, Tris

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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 PILATUS 2M / Detector: PIXEL / Date: Jun 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.2→59.65 Å / Num. obs: 40517 / % possible obs: 98.2 % / Redundancy: 2.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.028 / Rpim(I) all: 0.028 / Rrim(I) all: 0.039 / Net I/σ(I): 11.4
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3536 / CC1/2: 0.877 / Rpim(I) all: 0.309 / Rrim(I) all: 0.437 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
XDSJan 26, 2018data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2hvd

2hvd


Resolution: 2.2→59.65 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2201 1992 5.09 %
Rwork0.1713 37114 -
obs0.1738 39106 94.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.21 Å2 / Biso mean: 38.0417 Å2 / Biso min: 10.55 Å2
Refinement stepCycle: final / Resolution: 2.2→59.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7114 0 135 452 7701
Biso mean--46.12 36.12 -
Num. residues----895
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.260.3184860.22592041212772
2.26-2.320.30241290.23012250237982
2.32-2.380.25011540.20692622277695
2.38-2.460.28011260.2132811293799
2.46-2.550.27431430.21052746288999
2.55-2.650.251350.19482775291099
2.65-2.770.25271440.20232749289399
2.77-2.920.26411810.19612742292399
2.92-3.10.25341510.18262729288098
3.1-3.340.23331230.16762759288297
3.34-3.680.18451680.15562691285997
3.68-4.210.21951470.13672722286998
4.21-5.30.15041460.13582739288597
5.3-59.650.1881590.1622738289795
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9463-0.1076-0.07450.8031-0.34161.0076-0.0554-0.0985-0.10290.13610.0499-0.15210.1273-0.00790.0040.17880.0075-0.01920.11920.01810.173424.094710.1804103.3476
20.6184-0.03080.14950.8382-0.11310.7692-0.08330.05610.17920.0875-0.0047-0.1208-0.3474-0.01850.01940.27640.0032-0.02290.10.02770.212722.79636.566883.4394
30.83550.311-0.16870.74850.32221.1668-0.02140.2151-0.1657-0.1627-0.0304-0.22140.24960.01440.01310.2378-0.00210.0620.1741-0.04430.229925.82636.310170.3612
40.8973-0.2264-0.06820.4427-0.26071.2183-0.3179-0.3045-0.06640.21330.19780.17110.1472-0.98590.01510.0903-0.32010.16870.49310.12990.1898-0.0674.4315100.2721
51.23360.12580.44761.4274-0.39561.1312-0.01680.08680.18980.13240.04710.2054-0.3001-0.49-0.00810.21290.1884-0.00730.41290.01690.2493-0.439134.085683.6386
60.84710.0664-0.06090.66430.23570.96810.08070.2555-0.173-0.086-0.15190.1520.2683-0.5517-0.01030.2238-0.1213-0.06790.4962-0.13550.22991.35326.951467.457
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 201)A1 - 201
2X-RAY DIFFRACTION2(chain 'B' and resid 0 through 201)B0 - 201
3X-RAY DIFFRACTION3(chain 'C' and resid 1 through 201)C1 - 201
4X-RAY DIFFRACTION4(chain 'D' and resid 2 through 201)D2 - 201
5X-RAY DIFFRACTION5(chain 'E' and resid 1 through 152)E1 - 152
6X-RAY DIFFRACTION6(chain 'F' and resid 1 through 201)F1 - 201

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