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

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Basic information

Entry
Database: PDB / ID: 6rbz
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-(3-azanylpropyl)-8-bromanyl-purin-6-amine / NAD kinase 1
Similarity search - Component
Biological speciesListeria monocytogenes serovar 1/2a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.318 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)31,5093
Polymers31,0451
Non-polymers4632
Water54030
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)126,03412
Polymers124,1814
Non-polymers1,8538
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)62.120, 76.680, 118.510
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 serovar 1/2a (strain ATCC BAA-679 / 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-JXK / 9-(3-azanylpropyl)-8-bromanyl-purin-6-amine


Mass: 271.117 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H11BrN6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.27 Å3/Da / Density % sol: 45.88 %
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: ID30B / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.318→55.02 Å / Num. obs: 12508 / % possible obs: 98.8 % / Redundancy: 4.7 % / Biso Wilson estimate: 48.28 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.029 / Rrim(I) all: 0.064 / Net I/σ(I): 14.2 / Num. measured all: 58780
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
2.318-2.3584.90.6830356200.9320.3320.762.599.5
6.288-55.024.20.02528746860.9990.0140.02836.497.7

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.318→55.02 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.45
RfactorNum. reflection% reflection
Rfree0.2371 617 4.95 %
Rwork0.2136 --
obs0.2147 12465 98.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 129.61 Å2 / Biso mean: 62.806 Å2 / Biso min: 35.21 Å2
Refinement stepCycle: final / Resolution: 2.318→55.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2069 0 39 30 2138
Biso mean--97.34 55.69 -
Num. residues----262
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 (%)
2.3177-2.55090.32721420.2712931307399
2.5509-2.920.35181720.27132917308999
2.92-3.67880.29161450.23252965311099
3.6788-55.03510.17981580.18463035319397
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)
13.1594-0.8685-0.70522.0780.973.5515-0.047-0.98850.17860.0548-0.15930.1436-0.26140.1871-0.05760.59060.04950.01580.8528-0.06980.54778.519322.914128.6397
23.3164-0.9246-1.59411.53821.02623.53480.1145-0.5880.59560.10820.1104-0.1326-0.2163-0.0633-0.17750.55920.01060.06610.7384-0.11850.60114.570725.616219.7756
33.587-1.9554-1.48071.3320.78860.6638-0.05450.26880.7888-0.4289-0.08420.8931-0.4701-0.41370.03540.64840.05560.01310.86740.06950.66657.256420.3595-5.5192
41.52630.1224-0.1550.9960.97752.64990.09370.21430.0482-0.05790.01680.0786-0.0904-0.14580.00270.42890.02030.03720.45990.03420.427520.423911.3645-3.8126
55.08271.87650.99177.3272.35256.0074-0.1510.6875-0.1412-0.6280.5450.00180.5960.0216-0.1120.77450.0207-0.00240.74590.07930.463625.24571.4073-12.6022
62.9358-0.37240.27831.2873-0.40052.78760.26160.77260.37870.0084-0.20510.2515-0.027-0.48550.04880.45810.05420.0210.59450.02550.430317.063815.4222-10.5869
75.49360.28321.10944.26460.15473.6742-0.0995-0.382-0.19780.33660.02580.35480.8421-1.20780.02280.4528-0.07910.02560.75210.02510.61395.962910.7108-1.5225
83.0506-0.66050.84782.08980.66312.71680.0311-0.38210.40550.1151-0.0347-0.0734-0.1372-0.06930.06880.4741-0.01910.08240.5146-0.02370.505923.630219.749410.5463
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 102 )A27 - 102
3X-RAY DIFFRACTION3chain 'A' and (resid 103 through 120 )A103 - 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 230 )A217 - 230
8X-RAY DIFFRACTION8chain 'A' and (resid 231 through 264 )A231 - 264

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