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

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Basic information

Entry
Database: PDB / ID: 8qgn
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: 2.5 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)31,8783
Polymers31,0451
Non-polymers8332
Water68538
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)127,51212
Polymers124,1814
Non-polymers3,3318
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 area10660 Å2
ΔGint-44 kcal/mol
Surface area40690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.362, 75.709, 118.922
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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


Mass: 640.608 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H32N12O8 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.3 Å3/Da / Density % sol: 46.45 %
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: 0.8726 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.5→48.59 Å / Num. obs: 9955 / % possible obs: 98 % / Redundancy: 4.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.056 / Rrim(I) all: 0.129 / Net I/σ(I): 11.1 / Num. measured all: 45015
Reflection shellResolution: 2.5→2.59 Å / % possible obs: 99.2 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.629 / Num. measured all: 4389 / Num. unique obs: 974 / CC1/2: 0.817 / Rpim(I) all: 0.305 / Rrim(I) all: 0.704 / Net I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
SCALAdata scaling
XDSdata reduction
PHENIXphasing
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8A9V

8a9v


Resolution: 2.5→48.59 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2658 481 4.83 %
Rwork0.2087 --
obs0.2114 9953 97.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→48.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2063 0 59 38 2160
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092193
X-RAY DIFFRACTIONf_angle_d0.7662971
X-RAY DIFFRACTIONf_dihedral_angle_d16.3151284
X-RAY DIFFRACTIONf_chiral_restr0.054322
X-RAY DIFFRACTIONf_plane_restr0.003375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.590.2961740.2593119X-RAY DIFFRACTION98
2.8617-3.60530.25241560.22633141X-RAY DIFFRACTION98
3.6053-48.590.26281510.18483212X-RAY DIFFRACTION96
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)
12.8858-0.6505-1.68762.02791.23365.1294-0.1782-0.1574-0.01630.22070.01750.1905-0.1217-0.33690.18340.34570.09320.00430.4058-0.04490.337511.718123.105222.252
21.4181-0.2843-0.54551.83760.72244.860.028-0.26020.25510.0069-0.02020.0335-0.6136-0.14080.07580.26930.0673-0.02220.3673-0.02280.471316.227225.131412.6756
31.2988-0.1399-0.02511.92040.75473.43760.02370.0950.0548-0.0612-0.05070.21310.0589-0.26850.03270.20680.039-0.01630.23060.030.317218.585511.423-5.7412
42.6852-0.0853-0.2222.76551.3684.5904-0.2817-0.38310.22110.63890.1122-0.4635-0.29520.318-0.0510.4288-0.040.01540.3667-0.05870.361727.196519.697516.1046
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 79 )
2X-RAY DIFFRACTION2chain 'A' and (resid 80 through 120 )
3X-RAY DIFFRACTION3chain 'A' and (resid 121 through 238 )
4X-RAY DIFFRACTION4chain 'A' and (resid 239 through 264 )

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