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

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Basic information

Entry
Database: PDB / ID: 8qgo
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: 1.53 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)31,8913
Polymers31,0451
Non-polymers8462
Water2,414134
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)127,56412
Polymers124,1814
Non-polymers3,3838
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 area11390 Å2
ΔGint-39 kcal/mol
Surface area40090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.969, 74.436, 118.370
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-418-

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-UOL / 1-[[(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]methyl-methyl-amino]prop-1-ynyl]-6-azanyl-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl]-3-ethyl-urea


Mass: 653.650 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H35N13O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 44.94 %
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: 1.247→59.185 Å / Num. obs: 76054 / % possible obs: 98.66 % / Redundancy: 4.1 % / Biso Wilson estimate: 21.97 Å2 / Rmerge(I) obs: 0.029 / Rpim(I) all: 0.016 / Rrim(I) all: 0.034 / Net I/σ(I): 19.4
Reflection shellResolution: 1.247→1.393 Å / % possible obs: 10.7 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.865 / Num. measured all: 13615 / Num. unique obs: 2330 / Rpim(I) all: 0.391 / Rrim(I) all: 0.951 / Net I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8A9V

8a9v


Resolution: 1.53→55.59 Å / SU ML: 0.2014 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.3721
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2 3746 4.93 %
Rwork0.1616 72308 -
obs0.1635 76054 94.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.3 Å2
Refinement stepCycle: LAST / Resolution: 1.53→55.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2085 0 60 134 2279
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00662252
X-RAY DIFFRACTIONf_angle_d0.90993068
X-RAY DIFFRACTIONf_chiral_restr0.0614335
X-RAY DIFFRACTIONf_plane_restr0.0055421
X-RAY DIFFRACTIONf_dihedral_angle_d13.3366853
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.550.30491480.28732718X-RAY DIFFRACTION96.01
1.55-1.570.32751390.25652738X-RAY DIFFRACTION95.64
1.57-1.590.28261520.25042685X-RAY DIFFRACTION94.91
1.59-1.620.31621380.24412691X-RAY DIFFRACTION95.41
1.62-1.640.30911550.21632685X-RAY DIFFRACTION94.73
1.64-1.670.2781400.21472713X-RAY DIFFRACTION94.5
1.67-1.690.2141440.18342671X-RAY DIFFRACTION94.53
1.69-1.720.22371300.18762629X-RAY DIFFRACTION92.52
1.72-1.750.24871560.17562621X-RAY DIFFRACTION91.74
1.75-1.790.24821620.16152657X-RAY DIFFRACTION94.88
1.79-1.820.19031470.14862780X-RAY DIFFRACTION97.27
1.82-1.860.19611230.14612817X-RAY DIFFRACTION97.9
1.86-1.910.22051490.1942684X-RAY DIFFRACTION95.23
1.91-1.950.28121350.20762692X-RAY DIFFRACTION94.33
1.95-2.010.19311370.15612779X-RAY DIFFRACTION97.62
2.01-2.070.18851410.12772794X-RAY DIFFRACTION96.67
2.07-2.130.19881210.13452774X-RAY DIFFRACTION96.5
2.13-2.210.22251420.14162683X-RAY DIFFRACTION95.44
2.21-2.30.25331250.17912490X-RAY DIFFRACTION87.63
2.3-2.40.2091410.1542771X-RAY DIFFRACTION95.92
2.4-2.530.18531140.15272693X-RAY DIFFRACTION94.9
2.53-2.690.18551310.15352637X-RAY DIFFRACTION92.95
2.69-2.890.19391340.16712549X-RAY DIFFRACTION88.72
2.89-3.190.18511140.17032423X-RAY DIFFRACTION84.34
3.19-3.650.17881560.15142573X-RAY DIFFRACTION91.06
3.65-4.590.15171290.13382665X-RAY DIFFRACTION93.76
4.59-55.590.19151430.16672696X-RAY DIFFRACTION94.13

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