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- PDB-7r4l: Crystal structure of human mitochondrial NAD kinase -

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Basic information

Entry
Database: PDB / ID: 7r4l
TitleCrystal structure of human mitochondrial NAD kinase
ComponentsNAD kinase 2, mitochondrial
KeywordsTRANSFERASE / NADP bound form with iron
Function / homology
Function and homology information


NAD+ kinase / NADP biosynthetic process / NAD+ kinase activity / Nicotinate metabolism / NAD metabolic process / Mitochondrial protein degradation / mitochondrial matrix / phosphorylation / protein homodimerization activity / mitochondrion / ATP binding
Similarity search - Function
NAD kinase 2, mitochondrial / NAD kinase / ATP-NAD kinase, PpnK-type, C-terminal / ATP-NAD kinase N-terminal domain / Inorganic polyphosphate/ATP-NAD kinase, N-terminal / NAD kinase/diacylglycerol kinase-like domain superfamily
Similarity search - Domain/homology
: / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NAD kinase 2, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsLabesse, G. / Mary, C. / Gelin, M. / Lionne, C.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-17-CE18-0011-01 France
CitationJournal: Mol.Cell / Year: 2022
Title: Crystal structure of human NADK2 reveals a dimeric organization and active site occlusion by lysine acetylation.
Authors: Mary, C. / Soflaee, M.H. / Kesavan, R. / Gelin, M. / Brown, H. / Zacharias, G. / Mathews, T.P. / Lemoff, A. / Lionne, C. / Labesse, G. / Hoxhaj, G.
History
DepositionFeb 8, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 14, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD kinase 2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4893
Polymers44,6891
Non-polymers7992
Water2,972165
1
A: NAD kinase 2, mitochondrial
hetero molecules

A: NAD kinase 2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9776
Polymers89,3792
Non-polymers1,5994
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area6840 Å2
ΔGint-52 kcal/mol
Surface area29680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.406, 68.406, 223.224
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Components on special symmetry positions
IDModelComponents
11A-679-

HOH

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Components

#1: Protein NAD kinase 2, mitochondrial / Mitochondrial NAD kinase / NAD kinase domain-containing protein 1 / mitochondrial


Mass: 44689.320 Da / Num. of mol.: 1 / Fragment: Catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NADK2, C5orf33, MNADK, NADKD1 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4G0N4, NAD+ kinase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.83 Å3/Da / Density % sol: 56.6 % / Mosaicity: 0.1 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 400 28% v/v, CaCl2 150 mM, 0.1 M Sodium HEPES, 2% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.6→48.37 Å / Num. obs: 17069 / % possible obs: 99.5 % / Redundancy: 6.6 % / Biso Wilson estimate: 40.13 Å2 / CC1/2: 0.944 / Rmerge(I) obs: 0.517 / Rpim(I) all: 0.21 / Rrim(I) all: 0.558 / Net I/σ(I): 1.36
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.61-2.736.21.0511197219360.6720.4291.1441.298.7
9.05-221.514.50.03422124930.9970.0170.03833.898.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
Aimless0.7.7data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: alphafold

Resolution: 2.6→48.37 Å / SU ML: 0.3222 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.6867
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2351 860 5.04 %
Rwork0.178 16209 -
obs0.1809 17069 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.93 Å2
Refinement stepCycle: LAST / Resolution: 2.6→48.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2635 0 49 165 2849
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00752759
X-RAY DIFFRACTIONf_angle_d1.06243746
X-RAY DIFFRACTIONf_chiral_restr0.0883415
X-RAY DIFFRACTIONf_plane_restr0.0078483
X-RAY DIFFRACTIONf_dihedral_angle_d17.45151015
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.760.31271240.23042658X-RAY DIFFRACTION99.68
2.76-2.980.28121390.20882642X-RAY DIFFRACTION99.71
2.98-3.280.27741420.19542663X-RAY DIFFRACTION99.89
3.28-3.750.26121600.17442670X-RAY DIFFRACTION99.61
3.75-4.720.17951420.13692707X-RAY DIFFRACTION99.69
4.72-48.370.21151530.18542869X-RAY DIFFRACTION97.89
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)
15.52608559178-0.8886946062651.429937204585.88217573099-0.7314721045725.430112393660.2363271500570.6748047470680.569373694698-0.616742901533-0.01461578108170.105849438375-0.6657310200780.2545771102060.1003765784710.3193277554250.04262387171120.09509771511070.48522456170.09607944594350.418771176646-21.9510979282-5.5420817338123.3494055539
22.58225808845-0.600127311863-0.5682464153191.905752856080.9657750367452.650203490320.0185595923622-0.327312825020.08978986685930.1319422595880.0838020486188-0.007129409679030.002294259437350.0547972643956-0.1015885357170.183905513163-0.02713811987230.001610393112730.382272280540.05740070948110.303846741677-22.6132561395-15.802032290830.5440900251
31.99342042657-0.1590000514260.0676453964341.742194561560.1299985037633.4224563533-0.01492093771670.068085312675-0.170142521036-0.2051926681780.132472741921-0.1053144015710.4241397216540.280509284529-0.09862908350050.246786821479-0.000217283959664-0.01444967031580.2413986601120.02749446584860.326529391467-12.7643884736-27.89844483957.21151375047
42.643741135120.199622552943-0.7583273360361.023085059120.02274693899960.276622867-0.1462764094150.211534420064-0.00688597035615-0.155359439754-0.2065606824590.6520717760830.224749145935-0.5659043731160.0149735713380.538749230208-0.412833620618-0.2459547215041.039629572670.1678050440220.835309333699-45.1600511807-37.0227098001-2.02110485094
52.309509513891.110266712810.9350929137191.412087661031.240949794841.102671358840.173217745986-0.1188587516820.100152644414-0.08538386149460.02423900210550.517712124990.386998280437-1.01854975185-0.03496922713070.324617450998-0.16037288296-0.04753005365670.6036626527990.168096262230.530448371119-31.5330463378-35.244533968211.6605370819
62.80130823620.48692411854-1.13994769571.31830002641-1.015238487774.61599954045-0.006849329795950.590553575602-0.733899161557-0.516351142290.2024055616650.09786476594541.07068182213-0.178953014448-0.007742235770870.571434492725-0.0166716709839-0.05827283722720.337816559257-0.06981136779210.520351426156-17.1951573168-35.69146693750.111732739585
72.084560776520.547374709706-1.949433003731.65242751693-0.482253146226.88866908726-0.0841781419977-0.111858699605-0.231235728208-0.08268040164760.0408400440313-0.0529837589640.1915711556550.390193749892-0.0136155439140.1760898483490.0224647915848-0.03914248238870.2691738838860.01664680631670.328242258482-11.4214195943-26.718461413313.5065894727
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 64 through 109 )64 - 1091 - 32
22chain 'A' and (resid 110 through 221 )110 - 22133 - 144
33chain 'A' and (resid 222 through 327 )222 - 327145 - 227
44chain 'A' and (resid 328 through 349 )328 - 349228 - 245
55chain 'A' and (resid 350 through 377 )350 - 377246 - 273
66chain 'A' and (resid 378 through 402 )378 - 402274 - 298
77chain 'A' and (resid 403 through 441 )403 - 441299 - 337

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