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

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Basic information

Entry
Database: PDB / ID: 8qgi
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: 1.93 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)31,9963
Polymers31,0451
Non-polymers9512
Water2,126118
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)127,98512
Polymers124,1814
Non-polymers3,8048
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)62.915, 75.306, 118.523
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-448-

HOH

21A-507-

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-UZO / 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-(3-azanylpropyl)amino]prop-1-ynyl]-6-azanyl-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl]-3-(phenylmethyl)urea


Mass: 758.787 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H42N14O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.26 Å3/Da / Density % sol: 45.6 %
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-3 / Wavelength: 0.967697 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.967697 Å / Relative weight: 1
ReflectionResolution: 1.506→63.561 Å / Num. obs: 39441 / % possible obs: 98.4 % / Redundancy: 5.5 % / Biso Wilson estimate: 34.3 Å2 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.039 / Rrim(I) all: 0.096 / Net I/σ(I): 9.6
Reflection shellResolution: 1.934→1.968 Å / % possible obs: 9.7 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.955 / Num. measured all: 7991 / Num. unique obs: 1293 / Rpim(I) all: 0.411 / Rrim(I) all: 1.044 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→59.26 Å / SU ML: 0.1856 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.7616
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.214 1951 4.95 %
Rwork0.1876 37490 -
obs0.1889 39441 96.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.86 Å2
Refinement stepCycle: LAST / Resolution: 1.93→59.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2071 0 68 118 2257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00342212
X-RAY DIFFRACTIONf_angle_d0.63373000
X-RAY DIFFRACTIONf_chiral_restr0.0499323
X-RAY DIFFRACTIONf_plane_restr0.0041417
X-RAY DIFFRACTIONf_dihedral_angle_d14.0108837
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.980.30461390.27082693X-RAY DIFFRACTION97.59
1.98-2.040.25091430.25142701X-RAY DIFFRACTION97.53
2.04-2.10.28681320.23462702X-RAY DIFFRACTION97.99
2.1-2.160.24031310.22212700X-RAY DIFFRACTION97.86
2.16-2.240.24061370.2172680X-RAY DIFFRACTION97.27
2.24-2.330.25831460.2172684X-RAY DIFFRACTION95.48
2.33-2.440.21721330.20772657X-RAY DIFFRACTION97.89
2.44-2.570.23561310.19842736X-RAY DIFFRACTION98.08
2.57-2.730.21681440.20262690X-RAY DIFFRACTION97.93
2.73-2.940.2771600.20612651X-RAY DIFFRACTION97.13
2.94-3.230.22581580.20162667X-RAY DIFFRACTION97.55
3.23-3.70.19961260.16822702X-RAY DIFFRACTION96.75
3.7-4.660.18991460.15082651X-RAY DIFFRACTION96.38
4.66-59.260.16391250.17712576X-RAY DIFFRACTION92.75
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)
12.30731495265-0.352924192064-1.484740929931.005561570170.7969170553442.85541910735-0.0412861868238-0.420540329510.1799410489740.05630644206050.08744022721950.0426873789926-0.2641219955240.19070063058-0.0339757965270.4222014809280.0906757697130.02376954540290.436888999359-0.09091209866540.35561677249112.651191893623.734575215623.1818346171
21.74757277389-0.119468092479-0.2700138016471.58189590856-0.06021252612982.310378587230.05054621333560.1220500648210.0999346751933-0.0801306008138-0.035736784180.209784671911-0.0167382439963-0.273997646631-0.002996654620130.2358532918770.0281160848601-0.009442297147630.2485107136740.01236731103060.27602952629519.451493980713.3916239145-4.44276359003
31.72218776878-0.2182976038440.1534755197211.59655976431-0.1267448608162.0795214440.0376557917905-0.1290697236760.209840418140.0721137598921-0.01795795585360.196541397506-0.184749968315-0.254901234752-0.01501837064320.2987045151970.02900315911580.04543336085580.301881675327-0.03612574884330.3350524149119.074600389217.04593850787.29156018965
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 92 )1 - 921 - 92
22chain 'A' and (resid 93 through 216 )93 - 21693 - 213
33chain 'A' and (resid 217 through 264 )217 - 264214 - 261

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