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- PDB-6rg8: Crystal structure of NAD kinase 1 from Listeria monocytogenes in ... -

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Basic information

Entry
Database: PDB / ID: 6rg8
TitleCrystal structure of NAD kinase 1 from Listeria monocytogenes in complexe with an inhibitor
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
Probable inorganic polyphosphate/atp-NAD kinase; domain 2 / 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 / Tumour Suppressor Smad4 / Sandwich / Mainly Beta
Similarity search - Domain/homology
CITRIC ACID / Chem-K2K / NAD kinase 1
Similarity search - Component
Biological speciesListeria monocytogenes EGD-e (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 Å
AuthorsGelin, M. / Labesse, G.
CitationJournal: Acs Infect Dis. / Year: 2020
Title: From Substrate to Fragments to Inhibitor ActiveIn VivoagainstStaphylococcus aureus.
Authors: Gelin, M. / Paoletti, J. / Nahori, M.A. / Huteau, V. / Leseigneur, C. / Jouvion, G. / Dugue, L. / Clement, D. / Pons, J.L. / Assairi, L. / Pochet, S. / Labesse, G. / Dussurget, O.
History
DepositionApr 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2May 15, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id

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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)31,6893
Polymers31,0451
Non-polymers6442
Water90150
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)126,75512
Polymers124,1814
Non-polymers2,5748
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)63.047, 76.672, 119.162
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 (E. coli) / References: UniProt: Q8Y8D7, NAD+ kinase
#2: Chemical ChemComp-K2K / (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-[[4-(6-azanyl-9~{H}-purin-8-yl)but-3-ynylamino]methyl]oxolane-3,4-diol


Mass: 451.442 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H21N11O3
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O

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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: 2.32 Å3/Da / Density % sol: 46.97 % / Mosaicity: 1.3 °
Crystal growTemperature: 291.15 K / Method: evaporation / pH: 5
Details: 30 mM NaBr, 220 mM Kcitrate, glycerol 6%, 15-16% w/v PEG400

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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: MARRESEARCH / Detector: CCD / Date: Sep 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.47→59.58 Å / Num. obs: 10684 / % possible obs: 99.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 45.16 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.052 / Rrim(I) all: 0.137 / Net I/σ(I): 12.8 / Num. measured all: 72027 / Scaling rejects: 110
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.47-2.576.51.156765811730.730.4821.255298.8
8.91-59.585.50.03214192580.9990.0150.03636.797.5

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
MOSFLMdata reduction
Aimless0.7.1data scaling
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.47→55.728 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.27
RfactorNum. reflection% reflection
Rfree0.2419 531 4.99 %
Rwork0.201 --
obs0.2031 10638 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 127.29 Å2 / Biso mean: 55.0408 Å2 / Biso min: 24.05 Å2
Refinement stepCycle: final / Resolution: 2.47→55.728 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2074 0 46 50 2170
Biso mean--62.17 54.01 -
Num. residues----260
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4701-2.71860.31891330.26842471260499
2.7186-3.1120.30021220.237325212643100
3.112-3.92060.25471390.21342491263099
3.9206-55.74190.20221370.168726242761100
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)
12.7885-0.3391-1.63741.40391.04914.6094-0.0539-0.63250.28850.25420.04610.1165-0.2861-0.0398-0.06640.53320.08980.02240.5292-0.08970.348612.995424.212118.7499
21.8735-0.3286-0.20431.92780.58533.62450.07360.12630.1187-0.0355-0.02590.1599-0.0119-0.11570.03330.37420.03160.02620.26940.01590.242420.350313.0025-1.7538
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 122 )A1 - 122
2X-RAY DIFFRACTION2chain 'A' and (resid 123 through 263 )A123 - 263

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