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

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Basic information

Entry
Database: PDB / ID: 6rga
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-K3E / NAD kinase 1
Similarity search - Component
Biological speciesListeria monocytogenes EGD-e (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 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

Downloads & links

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Assembly

Deposited unit
A: NAD kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8073
Polymers31,0451
Non-polymers7622
Water1,60389
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)127,22812
Polymers124,1814
Non-polymers3,0478
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)63.180, 74.730, 118.730
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-436-

HOH

21A-480-

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-K3E / (2~{R},3~{S},4~{R},5~{R})-2-(aminomethyl)-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]oxolane-3,4-diol


Mass: 569.530 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H27N11O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 45.51 % / Mosaicity: 0.91 °
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: Dec 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.18→37.36 Å / Num. obs: 14968 / % possible obs: 99.7 % / Redundancy: 5.5 % / Biso Wilson estimate: 30.87 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.064 / Rrim(I) all: 0.152 / Net I/σ(I): 7.6 / Num. measured all: 83071 / Scaling rejects: 23
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
2.18-2.255.20.853666312770.7820.3970.9462.1100
8.99-37.365.10.08311882320.9940.0410.09317.294.1

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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: 2.18→34.975 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.05
RfactorNum. reflection% reflection
Rfree0.2385 758 5.07 %
Rwork0.2127 --
obs0.2141 14964 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 118.87 Å2 / Biso mean: 44.9591 Å2 / Biso min: 14.71 Å2
Refinement stepCycle: final / Resolution: 2.18→34.975 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2065 0 54 89 2208
Biso mean--35.52 42.22 -
Num. residues----259
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 (%)
2.1801-2.34840.35711560.317227922948100
2.3484-2.58470.2841580.247828012959100
2.5847-2.95850.27481620.239228282990100
2.9585-3.72670.22831290.200728753004100
3.7267-34.97920.19091530.17872910306398
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)
12.84-0.3287-1.74160.72440.85314.4301-0.1108-0.62290.28340.16480.07150.1527-0.3081-0.37190.11860.4740.12610.03960.5514-0.14980.357312.710423.894622.847
22.4493-0.475-1.60891.8997-0.94551.93210.2750.08960.7402-0.1707-0.17070.2784-0.9981-0.7155-0.00140.42920.21250.10260.4318-0.05530.395115.571825.95026.9792
32.2199-0.51830.36152.45840.50525.67630.07520.14760.002-0.0792-0.06270.23870.0773-0.46710.08610.13350.0237-0.00920.29650.0010.210618.95969.6661-5.0348
42.89920.28660.25982.7916-0.27533.36980.00580.25720.0824-0.1917-0.08390.39060.0093-0.32830.1310.1730.042-0.00970.26840.01230.17422.677311.3635-6.9756
50.647-0.12151.52782.74661.27984.54140.10340.15560.2755-0.0668-0.34020.96650.1095-1.45580.21640.25590.1161-0.02750.6954-0.10520.56839.228513.7168-3.5333
63.9646-1.4742-0.66464.19271.89392.1709-0.1566-0.73780.45730.65730.1247-0.3804-0.3138-0.131-0.01380.3625-0.04280.0340.291-0.1130.262427.383619.99716.272
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 89 )A1 - 89
2X-RAY DIFFRACTION2chain 'A' and (resid 90 through 120 )A90 - 120
3X-RAY DIFFRACTION3chain 'A' and (resid 121 through 167 )A121 - 167
4X-RAY DIFFRACTION4chain 'A' and (resid 168 through 216 )A168 - 216
5X-RAY DIFFRACTION5chain 'A' and (resid 217 through 238 )A217 - 238
6X-RAY DIFFRACTION6chain 'A' and (resid 239 through 264 )A239 - 264

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