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

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Basic information

Entry
Database: PDB / ID: 8qgh
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: 1.76 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)31,9623
Polymers31,0451
Non-polymers9172
Water1,31573
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)127,84812
Polymers124,1814
Non-polymers3,6678
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 area12050 Å2
ΔGint-36 kcal/mol
Surface area40260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.430, 73.850, 118.671
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-ULU / ~{N}-[3-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[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]amino]propyl]-3-[(azanylidene-$l^{4}-azanylidene)amino]propanamide


Mass: 724.708 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H38N15O8 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.24 Å3/Da / Density % sol: 45.05 %
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: 1.38→48.12 Å / Num. obs: 50202 / % possible obs: 97.77 % / Redundancy: 3.6 % / Biso Wilson estimate: 30.04 Å2 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.024 / Rrim(I) all: 0.046 / Net I/σ(I): 19.2
Reflection shellResolution: 1.38→1.552 Å / % possible obs: 8.3 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.726 / Num. measured all: 5811 / Num. unique obs: 1399 / Rpim(I) all: 0.397 / Rrim(I) all: 0.831 / 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
Starting model: 8A9V

8a9v


Resolution: 1.76→48.12 Å / SU ML: 0.2081 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.0153
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2267 2417 4.81 %
Rwork0.2098 47785 -
obs0.2106 50202 93.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.58 Å2
Refinement stepCycle: LAST / Resolution: 1.76→48.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2067 0 65 73 2205
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00212196
X-RAY DIFFRACTIONf_angle_d0.51142981
X-RAY DIFFRACTIONf_chiral_restr0.0455322
X-RAY DIFFRACTIONf_plane_restr0.0039412
X-RAY DIFFRACTIONf_dihedral_angle_d13.3394816
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.80.44021480.35172906X-RAY DIFFRACTION97.08
1.8-1.830.38411370.32942867X-RAY DIFFRACTION95.7
1.83-1.880.32911670.31152898X-RAY DIFFRACTION96.44
1.88-1.920.36471470.29962864X-RAY DIFFRACTION95.98
1.92-1.980.2581220.27722883X-RAY DIFFRACTION96.34
1.98-2.030.33741550.25392862X-RAY DIFFRACTION95.66
2.03-2.10.30451290.2442858X-RAY DIFFRACTION95.43
2.1-2.170.23361250.24052842X-RAY DIFFRACTION93.77
2.17-2.260.25711410.22962689X-RAY DIFFRACTION89.56
2.26-2.360.24481470.24112619X-RAY DIFFRACTION88.29
2.36-2.490.2631370.23662774X-RAY DIFFRACTION92.47
2.49-2.650.29341370.22492894X-RAY DIFFRACTION96.07
2.65-2.850.28081400.22212883X-RAY DIFFRACTION96.03
2.85-3.140.23951470.23882811X-RAY DIFFRACTION95.48
3.14-3.590.17171560.18672771X-RAY DIFFRACTION92.45
3.59-4.520.16271340.15962621X-RAY DIFFRACTION87.43
4.52-48.120.1951480.17792743X-RAY DIFFRACTION91.75
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)
14.05196030773-0.414478421292-2.420391472041.934267063871.951578122768.07533059399-0.137435523306-0.2987895553580.2397979283590.05948475609110.0763872916702-0.0576785588263-0.3440351286090.08342529609570.03365692292880.4465639779560.1118232864680.02427855319330.454856348148-0.1046192971030.34061827147313.131675118623.444666019823.5193612689
21.65684983675-0.08632165464680.03198539588841.8177471924-0.0471010347293.400391781210.05679472556270.07013460341120.09422380157890.0361817025043-0.08871305043210.168325594876-0.231922243955-0.4464323348220.07327151087330.2051791687370.06180821712260.009287866838770.269094339921-0.006064257971510.23626273068219.721917919913.031122486-3.38880888608
32.84994963229-1.85420447554-0.6934985416541.42310023353-0.4734381377245.228883665040.3508789123030.186589652804-0.2534668497690.241470679222-0.3474366916480.320211875991-0.0339904479094-0.9822254748040.0329593291510.2645870947960.09889160234460.004616506270270.363040889147-0.05967462078760.36395512929615.819374496514.104716532-8.03404255732
42.50964568617-0.8208597865590.7087407791131.096819299050.6378660667953.981690689160.0605954432157-0.270474585630.1685778336680.0528408236342-0.06477388194140.146202220135-0.340417017671-0.366898421560.02839634773660.3354392963050.0219703519740.06903739239750.287466883748-0.01140685253360.30239280617120.642155340718.05624981638.76713985301
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 198 )93 - 19893 - 198
33chain 'A' and (resid 199 through 221 )199 - 221199 - 221
44chain 'A' and (resid 222 through 264 )222 - 264222 - 264

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