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

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Basic information

Entry
Database: PDB / ID: 6rbp
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-(4-azidobutyl)purin-6-amine / NAD kinase 1
Similarity search - Component
Biological speciesListeria monocytogenes EGD-e (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.473 Å
AuthorsGelin, M. / Labesse, G.
Funding support France, 1items
OrganizationGrant numberCountry
France
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 / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)31,4703
Polymers31,0451
Non-polymers4242
Water63135
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)125,87912
Polymers124,1814
Non-polymers1,6978
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)62.970, 74.670, 118.880
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-410-

HOH

21A-423-

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-JYN / 9-(4-azidobutyl)purin-6-amine


Mass: 232.245 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12N8 / Feature type: SUBJECT OF INVESTIGATION
#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.: 35 / 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: 2.25 Å3/Da / Density % sol: 45.35 % / Mosaicity: 1.2 °
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: ID29 / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 2, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.47→55.65 Å / Num. obs: 10375 / % possible obs: 99.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 48.07 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.061 / Rrim(I) all: 0.12 / Net I/σ(I): 9.6 / Num. measured all: 38984 / Scaling rejects: 9
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
2.47-2.573.90.932451911680.8260.5411.0811.599.9
8.91-55.653.30.0338322540.990.0220.0433.398.2

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
Aimless0.7.1data scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementResolution: 2.473→55.65 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.78
RfactorNum. reflection% reflection
Rfree0.2366 767 9.99 %
Rwork0.2118 --
obs0.2143 7679 74.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 150.07 Å2 / Biso mean: 51.9907 Å2 / Biso min: 13.31 Å2
Refinement stepCycle: final / Resolution: 2.473→55.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2055 0 30 35 2120
Biso mean--61.68 47.4 -
Num. residues----260
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4734-2.66440.391380.312934238019
2.6644-2.93250.36641210.28841089121059
2.9325-3.35680.30931870.25931688187591
3.3568-4.22910.18892070.185518582065100
4.2291-63.25210.21872140.19541935214999
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)
13.30790.428-1.38461.1990.19575.10340.0992-0.46740.33260.0231-0.31020.0833-0.5731-0.29580.05940.49560.11510.05210.5172-0.13290.38929.794524.551622.2548
23.06071.9326-0.15361.76821.06245.0173-0.4637-1.04650.02510.11220.6901-0.0373-0.49170.7674-0.06540.54460.12280.11370.8987-0.17180.520720.537321.29926.4184
32.2253-1.5458-1.56971.93311.23834.81840.07210.00790.3177-0.0094-0.08550.3639-0.5982-0.4782-0.03680.2798-0.0320.03640.30920.02150.301414.831618.1452-1.4548
41.7593-0.3928-0.11511.8312-0.39532.20040.12190.22920.2615-0.1813-0.14680.1875-0.1179-0.13330.05230.11670.05080.00790.27070.01340.181923.165911.5801-2.3029
52.5489-0.2784-0.19722.3334-1.44822.26490.03110.2462-0.05-0.2326-0.0520.3916-0.0839-0.2270.13480.19170.0254-0.04010.26550.09190.185525.37539.7833-10.1229
61.7495-0.1793-0.59811.4644-0.25655.38470.10540.3950.06480.15340.29350.63550.8502-1.715-0.09270.30440.1778-0.06140.65150.08310.55237.993910.4312-6.819
71.2150.3445-0.17210.6361-1.34273.18230.5376-0.02020.76750.2348-0.00950.1592-1.074-0.114-0.19680.45110.23570.08650.4171-0.01170.457517.434524.46572.4351
82.67120.0876-1.16283.22860.17427.6141-0.0227-0.77960.80430.30830.0036-0.2428-0.4984-0.625-0.10090.3721-0.0078-0.00490.3986-0.08360.321230.61616.239319.1055
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 68 )A1 - 68
2X-RAY DIFFRACTION2chain 'A' and (resid 69 through 92 )A69 - 92
3X-RAY DIFFRACTION3chain 'A' and (resid 93 through 141 )A93 - 141
4X-RAY DIFFRACTION4chain 'A' and (resid 142 through 184 )A142 - 184
5X-RAY DIFFRACTION5chain 'A' and (resid 185 through 206 )A185 - 206
6X-RAY DIFFRACTION6chain 'A' and (resid 207 through 232 )A207 - 232
7X-RAY DIFFRACTION7chain 'A' and (resid 233 through 247 )A233 - 247
8X-RAY DIFFRACTION8chain 'A' and (resid 248 through 264 )A248 - 264

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