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

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Basic information

Entry
Database: PDB / ID: 8qgb
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: 2.27 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)31,9553
Polymers31,0451
Non-polymers9102
Water1,63991
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)127,82012
Polymers124,1814
Non-polymers3,6398
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)62.820, 75.780, 118.830
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-UTR / 2-[[(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]methylcarbamoyl]benzoic acid


Mass: 717.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H31N11O10 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.28 Å3/Da / Density % sol: 46 %
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: ID14-4 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.27→37.89 Å / Num. obs: 12967 / % possible obs: 96.3 % / Redundancy: 5.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.043 / Rrim(I) all: 0.099 / Χ2: 0.88 / Net I/σ(I): 14.5 / Num. measured all: 67319
Reflection shellResolution: 2.27→2.34 Å / % possible obs: 98.8 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.716 / Num. measured all: 5642 / Num. unique obs: 1202 / CC1/2: 0.713 / Rpim(I) all: 0.366 / Rrim(I) all: 0.808 / Χ2: 0.76 / Net I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
Aimlessdata scaling
MOSFLMdata reduction
PHENIXphasing
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.27→35.104 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2362 619 4.8 %
Rwork0.2082 --
obs0.2095 12909 95.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.27→35.104 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2029 0 65 91 2185
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152173
X-RAY DIFFRACTIONf_angle_d0.8072945
X-RAY DIFFRACTIONf_dihedral_angle_d17.1521283
X-RAY DIFFRACTIONf_chiral_restr0.065321
X-RAY DIFFRACTIONf_plane_restr0.003369
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2704-2.49880.3281730.27113062X-RAY DIFFRACTION98
2.4988-2.86020.25671460.22582998X-RAY DIFFRACTION94
2.8602-3.6030.19921450.2093073X-RAY DIFFRACTION96
3.603-35.1040.22181550.18653157X-RAY DIFFRACTION95
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)
11.8168-0.6109-1.34831.59340.62423.3795-0.0543-0.2230.13740.37070.140.1301-0.18630.0421-0.08180.42750.11990.04150.413-0.04940.338913.047824.353519.0251
21.1493-0.33850.06861.78980.60163.14080.04630.05120.05670.0181-0.0690.2483-0.069-0.27760.06450.17970.02810.02440.22690.01340.238920.032212.8944-1.7659
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 122 )
2X-RAY DIFFRACTION2chain 'A' and (resid 123 through 263 )

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