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

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Basic information

Entry
Database: PDB / ID: 8qgg
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: 1.59 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)31,9574
Polymers31,0451
Non-polymers9123
Water1,76598
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)127,82816
Polymers124,1814
Non-polymers3,64712
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 area12340 Å2
ΔGint-38 kcal/mol
Surface area39880 Å2
Unit cell
Length a, b, c (Å)62.898, 74.279, 118.386
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-UJT / (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-[[3-[6-azanyl-9-[(2~{R},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]purin-8-yl]prop-2-ynyl-(3-oxidanylpropyl)amino]methyl]oxolane-3,4-diol


Mass: 627.609 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H33N11O8 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 44.77 %
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: 0.96546 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 1.282→55.55 Å / Num. obs: 69703 / % possible obs: 99.28 % / Redundancy: 5.3 % / Biso Wilson estimate: 25.62 Å2 / Rmerge(I) obs: 0.032 / Rpim(I) all: 0.015 / Rrim(I) all: 0.035 / Net I/σ(I): 21.3
Reflection shellResolution: 1.592→1.619 Å / Redundancy: 7 % / Rmerge(I) obs: 1.085 / Num. unique obs: 2016 / Rpim(I) all: 0.44

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.59→55.55 Å / SU ML: 0.1871 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.9295
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2165 3439 4.93 %
Rwork0.1782 66264 -
obs0.18 69703 97.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.69 Å2
Refinement stepCycle: LAST / Resolution: 1.59→55.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2078 0 64 99 2241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00542228
X-RAY DIFFRACTIONf_angle_d0.84453020
X-RAY DIFFRACTIONf_chiral_restr0.0558325
X-RAY DIFFRACTIONf_plane_restr0.0057413
X-RAY DIFFRACTIONf_dihedral_angle_d15.3403847
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.610.29041700.27062671X-RAY DIFFRACTION99.02
1.61-1.640.30231670.24792646X-RAY DIFFRACTION98.39
1.64-1.660.27821100.24942721X-RAY DIFFRACTION98.09
1.66-1.690.28361280.22552649X-RAY DIFFRACTION97.99
1.69-1.710.2831470.22132674X-RAY DIFFRACTION97.99
1.71-1.740.27491690.20152658X-RAY DIFFRACTION97.48
1.74-1.780.26671790.19462655X-RAY DIFFRACTION97.96
1.78-1.810.22591180.19752693X-RAY DIFFRACTION97.74
1.81-1.850.22361180.16992663X-RAY DIFFRACTION97.96
1.85-1.890.22291380.17442654X-RAY DIFFRACTION97.49
1.89-1.930.27271530.19112643X-RAY DIFFRACTION97.29
1.93-1.980.16891240.15662670X-RAY DIFFRACTION97.45
1.98-2.030.2121070.15132728X-RAY DIFFRACTION97.42
2.03-2.090.22631450.15442630X-RAY DIFFRACTION97.2
2.09-2.160.21951400.16192666X-RAY DIFFRACTION97.33
2.16-2.240.24121450.16352649X-RAY DIFFRACTION97.76
2.24-2.330.21981170.16562721X-RAY DIFFRACTION97.06
2.33-2.430.23591420.16712628X-RAY DIFFRACTION97.74
2.43-2.560.19621540.16332664X-RAY DIFFRACTION97.27
2.56-2.720.26251280.17912594X-RAY DIFFRACTION95.31
2.72-2.930.24431250.19382589X-RAY DIFFRACTION94.8
2.93-3.230.24541150.19662611X-RAY DIFFRACTION94.75
3.23-3.690.1981320.16792525X-RAY DIFFRACTION92.45
3.69-4.650.19271210.15592601X-RAY DIFFRACTION94.48
4.65-55.550.17931470.19522661X-RAY DIFFRACTION97.36

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