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

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Basic information

Entry
Database: PDB / ID: 8qgj
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: 2.29 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

Downloads & links

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Assembly

Deposited unit
A: NAD kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9343
Polymers31,0451
Non-polymers8892
Water77543
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)127,73612
Polymers124,1814
Non-polymers3,5558
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
Unit cell
Length a, b, c (Å)63.020, 74.914, 118.490
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
Components on special symmetry positions
IDModelComponents
11A-415-

HOH

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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-UX6 / ~{N}-[[(2~{R},3~{S},4~{R},5~{R})-5-[8-[3-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy]prop-1-ynyl]-6-azanyl-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl]-4-carbamimidamido-butanamide


Mass: 696.674 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H36N14O8 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.25 Å3/Da / Density % sol: 45.39 %
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: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 2.29→63.32 Å / Num. obs: 22928 / % possible obs: 97.4 % / Redundancy: 4.8 % / Biso Wilson estimate: 38.14 Å2 / CC1/2: 0.981 / Rpim(I) all: 0.142 / Rrim(I) all: 0.331 / Χ2: 1.01 / Net I/σ(I): 6.3
Reflection shellResolution: 2.29→2.37 Å / Redundancy: 4.7 % / Rmerge(I) obs: 1.712 / Num. unique obs: 1161 / CC1/2: 0.683 / Rpim(I) all: 0.815 / Χ2: 0.81

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.29→63.32 Å / SU ML: 0.3862 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.8857
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2658 1157 5.05 %
Rwork0.2257 21771 -
obs0.2276 22928 93.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.94 Å2
Refinement stepCycle: LAST / Resolution: 2.29→63.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2074 0 63 43 2180
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00332195
X-RAY DIFFRACTIONf_angle_d0.60162974
X-RAY DIFFRACTIONf_chiral_restr0.0477321
X-RAY DIFFRACTIONf_plane_restr0.0032408
X-RAY DIFFRACTIONf_dihedral_angle_d15.8063826
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.390.37051460.35812606X-RAY DIFFRACTION89.23
2.39-2.520.38941570.32492687X-RAY DIFFRACTION93.52
2.52-2.680.35271650.30422690X-RAY DIFFRACTION93.42
2.68-2.880.34271640.30642759X-RAY DIFFRACTION95.43
2.88-3.170.34751440.27342750X-RAY DIFFRACTION95.1
3.17-3.630.23431370.21742765X-RAY DIFFRACTION95.12
3.63-4.580.19581240.16952735X-RAY DIFFRACTION93.49
4.58-63.320.18531200.17442779X-RAY DIFFRACTION94.28
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)
12.25802531042-0.492928351265-1.538423256750.9152850652140.5044477026993.287157475770.0536371681733-0.345724433310.1503281294390.2000483943740.0017543816870.133774182504-0.1847236789410.139161607688-0.01562503972010.4306507164280.0475678070940.03820797028630.430557405714-0.04319067932740.39343664043113.002113291623.912786991719.1395696236
21.27632084993-0.302606029344-0.01038585742621.83102944070.1118099186432.537357009730.08498446345840.02967428338870.053075880673-0.0862866238652-0.05845524727540.123268742226-0.0784786910757-0.280489205932-0.005436163326420.243488425040.03947467989460.01512669936040.3393569676220.006608066877660.31038113732820.278486161913.023625088-1.25897686215
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 1 through 120 )1 - 1201 - 117
22chain 'A' and (resid 121 through 264 )121 - 264118 - 261

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