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

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Basic information

Entry
Database: PDB / ID: 6rbt
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 / 8-bromanyl-9-(4-bromanylbutyl)purin-6-amine / NAD kinase 1
Similarity search - Component
Biological speciesListeria monocytogenes EGD-e (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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)31,5863
Polymers31,0451
Non-polymers5412
Water724
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)126,34612
Polymers124,1814
Non-polymers2,1658
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 area9220 Å2
ΔGint-48 kcal/mol
Surface area41600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.521, 76.178, 117.998
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-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-JXE / 8-bromanyl-9-(4-bromanylbutyl)purin-6-amine


Mass: 349.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11Br2N5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 45.64 % / Mosaicity: 0.22 °
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: 0.97625 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.55→48.33 Å / Num. obs: 9476 / % possible obs: 99.6 % / Redundancy: 6.5 % / Biso Wilson estimate: 63.81 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.039 / Rrim(I) all: 0.098 / Net I/σ(I): 11 / Num. measured all: 61381
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
2.55-2.646.60.98159599080.8820.4121.0651.799.7
9.88-48.335.30.0510291940.990.0270.05830.998.7

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
SCALA0.5.31data scaling
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→48.328 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 40.44
RfactorNum. reflection% reflection
Rfree0.2938 423 4.47 %
Rwork0.2477 --
obs0.2498 9461 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 162.26 Å2 / Biso mean: 86.1005 Å2 / Biso min: 46.64 Å2
Refinement stepCycle: final / Resolution: 2.55→48.328 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2056 0 29 4 2089
Biso mean--121.38 64.4 -
Num. residues----261
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.55-2.91890.38961230.34492960308399
2.9189-3.67740.33911500.28062978312899
3.6774-48.3370.26491500.219631003250100
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)
14.1120.05830.52964.1585-0.21014.10340.2713-0.8187-0.13590.0932-0.3321-0.2503-0.4087-0.13040.05090.75620.11970.02481.0384-0.00830.73448.574522.71828.5663
25.25660.0491.92631.3068-2.11494.3185-0.2199-0.52860.65470.3539-0.13660.3161-0.2187-0.04210.17490.62340.06310.1081.0726-0.17850.84398.301929.888922.8742
33.8248-0.3621-1.74245.99921.34945.147-0.47120.4238-0.20250.2597-0.04530.60170.449-0.73650.27290.51770.05680.05160.8812-0.10390.64569.842222.050912.4612
44.6649-2.9256-2.79734.66713.05763.4138-0.6067-0.31640.01690.62370.2752-0.1836-0.0865-0.20910.41430.7921-0.02140.1170.9276-0.00930.690118.647220.229419.5325
53.2099-0.19990.30282.19830.33426.71630.1828-1.14010.58840.86740.2126-0.4371-1.6264-0.1535-0.09220.80670.01650.10360.982-0.16070.888120.57129.00323.1884
62.8809-0.4235-0.49612.94651.73996.33890.28690.43420.1202-0.1546-0.23180.52980.0858-0.28920.080.6043-0.01390.01060.89220.04820.653512.338914.2848-6.3036
71.79220.9171.41731.56720.60123.20380.08950.17830.1926-0.04090.15310.052-0.246-0.3443-0.33330.46730.05930.06340.6673-0.02080.580823.287212.0234-1.7077
83.5368-0.70860.04643.0761-1.11113.54510.28960.4382-0.2621-0.1264-0.18210.42440.3826-0.7683-0.13850.54440.0562-0.02720.8240.02130.625515.892610.0127-7.9033
96.5139-1.80941.4443.15620.25056.26260.0167-0.24120.29390.0335-0.0574-0.0355-0.03980.20340.28190.506-0.03010.1130.4921-0.05570.639423.591119.504810.1856
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 44 )A27 - 44
3X-RAY DIFFRACTION3chain 'A' and (resid 45 through 58 )A45 - 58
4X-RAY DIFFRACTION4chain 'A' and (resid 59 through 79 )A59 - 79
5X-RAY DIFFRACTION5chain 'A' and (resid 80 through 102 )A80 - 102
6X-RAY DIFFRACTION6chain 'A' and (resid 103 through 141 )A103 - 141
7X-RAY DIFFRACTION7chain 'A' and (resid 142 through 184 )A142 - 184
8X-RAY DIFFRACTION8chain 'A' and (resid 185 through 230 )A185 - 230
9X-RAY DIFFRACTION9chain 'A' and (resid 231 through 264 )A231 - 264

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