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- PDB-8qg9: Crystal structure of NAD kinase 1 from Listeria monocytogenes in ... -

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Basic information

Entry
Database: PDB / ID: 8qg9
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: 1.79 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)31,8493
Polymers31,0451
Non-polymers8042
Water1,47782
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)127,39612
Polymers124,1814
Non-polymers3,2158
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)62.911, 74.155, 118.345
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-UWF / (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-propan-2-yl-amino]methyl]oxolane-3,4-diol


Mass: 611.610 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H33N11O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.22 Å3/Da / Density % sol: 44.67 %
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: ID29 / Wavelength: 0.96863 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 1.79→47.97 Å / Num. obs: 25864 / % possible obs: 97.7 % / Redundancy: 6.8 % / Biso Wilson estimate: 30.25 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.029 / Rrim(I) all: 0.076 / Net I/σ(I): 13.2 / Num. measured all: 177164
Reflection shellResolution: 1.79→1.85 Å / % possible obs: 84.9 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.943 / Num. measured all: 10569 / Num. unique obs: 2166 / CC1/2: 0.752 / Rpim(I) all: 0.445 / Rrim(I) all: 1.05 / Net I/σ(I) obs: 1.4

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
SCALAdata scaling
XDSdata reduction
PHENIXphasing
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→47.97 Å / SU ML: 0.2114 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.2509
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2403 1310 5.07 %
Rwork0.2102 24513 -
obs0.2117 25823 97.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.55 Å2
Refinement stepCycle: LAST / Resolution: 1.79→47.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2038 0 57 83 2178
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01052181
X-RAY DIFFRACTIONf_angle_d1.21192962
X-RAY DIFFRACTIONf_chiral_restr0.0877326
X-RAY DIFFRACTIONf_plane_restr0.0086372
X-RAY DIFFRACTIONf_dihedral_angle_d14.6527787
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.860.33031260.32322337X-RAY DIFFRACTION84.67
1.86-1.950.24711480.26572631X-RAY DIFFRACTION96.43
1.95-2.050.25551500.2412732X-RAY DIFFRACTION99.24
2.05-2.180.27511560.22732749X-RAY DIFFRACTION99.32
2.18-2.350.24491430.20242744X-RAY DIFFRACTION99.45
2.35-2.580.24121390.20512787X-RAY DIFFRACTION99.35
2.58-2.960.25451570.21952766X-RAY DIFFRACTION99.32
2.96-3.720.21761510.20852812X-RAY DIFFRACTION99.5
3.72-47.970.23391400.19352955X-RAY DIFFRACTION99.81
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)
12.07855121285-0.161103591398-0.7951709467281.491629414620.989856037263.01736483537-0.113808106949-0.190601768160.1806847823780.161536004536-0.09011410564930.198709224484-0.203165995066-0.4512096295670.1080286447690.4593797096520.1199926388890.05008043921880.422001106318-0.08444355168470.35890531732411.879432339123.038145217522.0195272427
21.08890371336-0.27500613472-1.062277069731.743616296330.08232769513792.370204774720.17041676563-0.08978848135050.463161173256-0.0468803716226-0.08430094338190.0827827907013-0.906273790829-0.6776341319980.1489382988870.3185535991390.1539837526420.04809820483060.482211151216-0.06386483133510.41089256900415.421167813524.463363954310.990397968
31.19032711808-0.5584735674640.2690722884532.057252458120.04102769312673.580990819760.07023318767330.159015694607-0.0236965862727-0.121280708301-0.07898642192710.2557660991590.185983163296-0.1835232148970.04757597744470.2009720766910.0155785426665-0.003611208139380.270682359116-0.02518244226080.26337924771518.76790076669.84420245083-5.35060846815
41.52114387991-0.281266227152-0.2125685193682.73666001159-0.8327415006582.872426598310.05820766982960.159606081383-0.0081623695976-0.363457136844-0.0939921938220.2975202823770.082484123241-0.1999680926970.06798719121930.1974700892320.0617197499729-0.001769067688470.248563176018-0.002708013682710.25672878121722.541321445111.5636190513-6.71263694627
51.61522440122-0.496226746644-0.01369860852821.45333680898-0.3245418018332.976839136580.115237943057-0.1657909809630.01049442909380.207689552771-0.06562851250130.282304748424-0.183651538664-0.5800955566930.02570019663230.3186473294510.07425795497410.05247610224490.391943260352-0.04154157461860.42554309065114.455085425318.69984351053.52223913381
64.199600362740.497271056370.2891762154065.185632292160.4253120434624.563493662410.0520482141303-0.6478397175410.1084253157840.700216445338-0.006215703215210.1918157405470.1569286960810.3635961739760.05955884608680.300631272913-0.0092137709910.04237491810970.283871687686-0.04259575238160.27664089667131.615275910712.93096959117.3229633207
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 79 )1 - 791 - 79
22chain 'A' and (resid 80 through 120 )80 - 12080 - 114
33chain 'A' and (resid 121 through 166 )121 - 166115 - 160
44chain 'A' and (resid 167 through 216 )167 - 216161 - 210
55chain 'A' and (resid 217 through 252 )217 - 252211 - 246
66chain 'A' and (resid 253 through 264 )253 - 264247 - 258

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