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- PDB-8qgm: Crystal structure of NAD kinase 1 from Listeria monocytogenes in ... -

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Basic information

Entry
Database: PDB / ID: 8qgm
TitleCrystal structure of NAD kinase 1 from Listeria monocytogenes in complex with a di-adenosine derivative
ComponentsNAD kinase 1
KeywordsTRANSFERASE / tetrameric NAD-kinase
Function / homology
Function and homology information


NAD+ kinase / NAD+ kinase activity / NADP+ biosynthetic process / NAD+ metabolic process / NAD binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
ATP-NAD kinase C-terminal domain / NAD kinase / ATP-NAD kinase, PpnK-type, C-terminal / ATP-NAD kinase N-terminal domain / NAD kinase/diacylglycerol kinase-like domain superfamily / Inorganic polyphosphate/ATP-NAD kinase, N-terminal
Similarity search - Domain/homology
CITRIC ACID / : / NAD kinase 1
Similarity search - Component
Biological speciesListeria monocytogenes EGD-e (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsGelin, M. / Labesse, G. / Lionne, C.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-17-CE18-0011-02 France
CitationJournal: To Be Published
Title: Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with a di-adenosine derivative
Authors: Gelin, M. / Labesse, G. / Clement, D. / Pochet, S. / Lionne, C. / Leseigneur, C. / Huteau, V.
History
DepositionSep 5, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NAD kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9273
Polymers31,0451
Non-polymers8822
Water1,53185
1
A: NAD kinase 1
hetero molecules

A: NAD kinase 1
hetero molecules

A: NAD kinase 1
hetero molecules

A: NAD kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,70812
Polymers124,1814
Non-polymers3,5278
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area12810 Å2
ΔGint-46 kcal/mol
Surface area40110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.850, 74.354, 118.435
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein NAD kinase 1 / ATP-dependent NAD kinase


Mass: 31045.279 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes EGD-e (bacteria)
Gene: nadK1, lmo0968 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8Y8D7, NAD+ kinase
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-V0I / 8-[3-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-methyl-amino]prop-1-ynyl]-6-azanyl-9-[(2~{R},3~{R},4~{S},5~{R})-5-[(dimethylsulfamoylamino)methyl]-3,4-bis(oxidanyl)oxolan-2-yl]purine


Mass: 689.703 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H35N13O8S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.23 Å3/Da / Density % sol: 44.8 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 30 mM NaBr, 220 mM Kcitrate, glycerol 6%, 15-16% w/v PEG400
PH range: 4.8-5.1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965459 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965459 Å / Relative weight: 1
ReflectionResolution: 1.333→62.973 Å / Num. obs: 56722 / % possible obs: 91.58 % / Redundancy: 4.7 % / Biso Wilson estimate: 26.12 Å2 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.021 / Rrim(I) all: 0.046 / Net I/σ(I): 16.6
Reflection shellResolution: 1.657→1.685 Å / % possible obs: 9.2 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.777 / Num. measured all: 6271 / Num. unique obs: 1698 / Rpim(I) all: 0.443 / Rrim(I) all: 0.901 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.66→62.97 Å / SU ML: 0.2118 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.8383
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2013 2863 5.05 %
Rwork0.1588 53859 -
obs0.1611 56722 88.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.88 Å2
Refinement stepCycle: LAST / Resolution: 1.66→62.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2074 0 61 85 2220
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01042203
X-RAY DIFFRACTIONf_angle_d1.15172990
X-RAY DIFFRACTIONf_chiral_restr0.0719324
X-RAY DIFFRACTIONf_plane_restr0.0072410
X-RAY DIFFRACTIONf_dihedral_angle_d15.5889825
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.690.38351640.34492937X-RAY DIFFRACTION98.2
1.69-1.720.3481290.31232978X-RAY DIFFRACTION97.92
1.72-1.750.31281760.27522984X-RAY DIFFRACTION97.59
1.75-1.780.26741570.24312954X-RAY DIFFRACTION98.05
1.78-1.820.2441380.21322972X-RAY DIFFRACTION98.14
1.82-1.870.26731460.19882919X-RAY DIFFRACTION95.01
1.87-1.870.092420.173213X-RAY DIFFRACTION19.48
1.94-1.960.2449640.19351562X-RAY DIFFRACTION95.14
1.96-2.020.26121660.17852955X-RAY DIFFRACTION96.84
2.02-2.090.23151490.18342857X-RAY DIFFRACTION95.95
2.09-2.160.21781680.1532891X-RAY DIFFRACTION96.13
2.16-2.250.22961640.16062834X-RAY DIFFRACTION93.72
2.25-2.350.22681490.14582926X-RAY DIFFRACTION96.3
2.35-2.470.2091400.16252931X-RAY DIFFRACTION96.75
2.48-2.630.17621590.15912938X-RAY DIFFRACTION97.21
2.63-2.830.23811420.15782899X-RAY DIFFRACTION95.6
2.83-3.120.18351400.16382874X-RAY DIFFRACTION94.45
3.12-3.570.19391570.1432811X-RAY DIFFRACTION93.45
3.57-4.490.14611450.12692765X-RAY DIFFRACTION90.6
4.5-62.970.19312080.14382859X-RAY DIFFRACTION96.17

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