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

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Basic information

Entry
Database: PDB / ID: 6rbu
TitleCrystal structure of NAD kinase 1 from Listeria monocytogenes in complexe with an adenine 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
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 / 9-(2-azidoethyl)-8-bromanyl-purin-6-amine / NAD kinase 1
Similarity search - Component
Biological speciesListeria monocytogenes EGD-e (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 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 11, 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

Downloads & links

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Assembly

Deposited unit
A: NAD kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5203
Polymers31,0451
Non-polymers4752
Water1,53185
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)126,08212
Polymers124,1814
Non-polymers1,9018
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)62.552, 75.988, 118.247
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-418-

HOH

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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-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-JYK / 9-(2-azidoethyl)-8-bromanyl-purin-6-amine


Mass: 283.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7BrN8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.26 Å3/Da / Density % sol: 45.65 %
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: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.448→55.292 Å / Num. obs: 25869 / % possible obs: 93.8 % / Redundancy: 4.3 % / CC1/2: 1 / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.018 / Rrim(I) all: 0.038 / Net I/σ(I): 19.3 / Num. measured all: 112187
Reflection shell

Num. unique obs: 1293 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.448-1.6245.40.68769300.7750.320.761.982.8
5.038-55.2924.10.01652750.9990.0090.01857.298

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→55.292 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 32.05
RfactorNum. reflection% reflection
Rfree0.2628 970 5.02 %
Rwork0.2261 --
obs0.228 19327 95.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 116.03 Å2 / Biso mean: 48.7001 Å2 / Biso min: 20.91 Å2
Refinement stepCycle: final / Resolution: 1.97→55.292 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2076 0 29 85 2190
Biso mean--78.6 48.56 -
Num. residues----261
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9699-2.07380.38411510.28332639279098
2.0738-2.20370.30071190.30132574269394
2.2037-2.37390.47991210.43042184230581
2.3739-2.61280.31611500.25222699284999
2.6128-2.99080.28281410.25162704284598
2.9908-3.7680.22361300.19962720285098
3.768-55.3140.20191580.17222837299598
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)
13.5625-0.783-0.49611.21180.73293.4149-0.1769-0.6640.0190.0664-0.00770.3692-0.1997-0.31090.03280.4270.11920.06380.5306-0.10520.33448.692622.65228.6105
22.8675-0.4481-1.13661.45660.59622.1389-0.0858-0.42110.40830.2110.096-0.03-0.1425-0.1391-0.0120.44270.07650.04960.4836-0.12810.399613.750224.625320.5934
31.4363-0.2351-0.83781.1581-0.28270.64160.1348-0.03210.8336-0.0086-0.14670.5018-0.6803-0.6769-0.06360.4240.09670.09520.3959-0.0230.505213.977525.22784.275
41.6515-0.2045-0.24490.83950.4952.71520.02540.14960.0381-0.0248-0.07690.1552-0.0577-0.21730.04980.26530.01790.0180.27260.00410.279420.72711.4387-3.7497
51.77960.63740.31043.59540.66553.850.06220.2862-0.3173-0.72750.26410.12060.2745-0.1921-0.05430.55180.0308-0.0190.40030.0050.316725.46121.3015-12.6787
62.4628-1.0501-0.46791.2597-1.12682.26050.18350.3081-0.2389-0.0913-0.06170.26150.31-0.6746-0.03180.36880.029-0.01520.39860.02280.364717.244415.3717-10.5435
72.0398-0.7462-0.06531.65940.54972.3485-0.0145-0.36010.19470.1425-0.02310.1624-0.2392-0.53110.06780.28530.01640.07780.2694-0.02320.29118.912817.07167.2467
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 26 )A1 - 26
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 91 )A27 - 91
3X-RAY DIFFRACTION3chain 'A' and (resid 92 through 120 )A92 - 120
4X-RAY DIFFRACTION4chain 'A' and (resid 121 through 184 )A121 - 184
5X-RAY DIFFRACTION5chain 'A' and (resid 185 through 198 )A185 - 198
6X-RAY DIFFRACTION6chain 'A' and (resid 199 through 216 )A199 - 216
7X-RAY DIFFRACTION7chain 'A' and (resid 217 through 264 )A217 - 264

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