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- PDB-6rc0: Crystal structure of NAD kinase 1 from Listeria monocytogenes in ... -

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Basic information

Entry
Database: PDB / ID: 6rc0
TitleCrystal structure of NAD kinase 1 from Listeria monocytogenes in complexe with an adenine derivative
ComponentsNAD kinase 1NAD+ kinase
KeywordsTRANSFERASE / tetrameric NAD kinase
Function / homology
Function and homology information


NAD+ kinase / NADP biosynthetic process / NAD+ kinase activity / NAD metabolic process / NAD binding / phosphorylation / 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 / Inorganic polyphosphate/ATP-NAD kinase, N-terminal / NAD kinase/diacylglycerol kinase-like domain superfamily / Tumour Suppressor Smad4 / Sandwich / Mainly Beta
Similarity search - Domain/homology
CITRIC ACID / 8-bromanyl-9-[(2~{R})-oxan-2-yl]purin-6-amine / NAD kinase 1
Similarity search - Component
Biological speciesListeria monocytogenes serovar 1/2a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 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

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Assembly

Deposited unit
A: NAD kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5363
Polymers31,0451
Non-polymers4902
Water61334
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)126,14212
Polymers124,1814
Non-polymers1,9618
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 area9920 Å2
ΔGint-50 kcal/mol
Surface area41330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.110, 78.190, 117.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein NAD kinase 1 / NAD+ kinase / 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)
Strain: ATCC BAA-679 / EGD-e / Gene: nadK1, lmo0968 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8Y8D7, NAD+ kinase
#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-JXH / 8-bromanyl-9-[(2~{R})-oxan-2-yl]purin-6-amine


Mass: 298.139 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12BrN5O
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.31 Å3/Da / Density % sol: 46.67 % / Mosaicity: 0.81 °
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: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.47→37.52 Å / Num. obs: 9737 / % possible obs: 91.4 % / Redundancy: 5.4 % / Biso Wilson estimate: 40.23 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.193 / Rpim(I) all: 0.091 / Rrim(I) all: 0.214 / Net I/σ(I): 7 / Num. measured all: 52342 / Scaling rejects: 42
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.47-2.575.51.17810350.4540.6271.30299.9
2.47-35.134.30.03197360.9990.0170.03598.7

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
ADSCdata collection
Aimless0.7.1data scaling
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→37.522 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2521 334 4.63 %
Rwork0.2263 --
obs0.2275 7210 92.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.75→37.522 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2073 0 30 34 2137
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052181
X-RAY DIFFRACTIONf_angle_d0.6582956
X-RAY DIFFRACTIONf_dihedral_angle_d19.7351291
X-RAY DIFFRACTIONf_chiral_restr0.047317
X-RAY DIFFRACTIONf_plane_restr0.003379
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7502-3.46450.3061750.27493453X-RAY DIFFRACTION100
3.4645-37.52590.2271590.20583423X-RAY DIFFRACTION91
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)
13.7004-1.6666-1.83442.68681.61093.3043-0.0235-0.4483-0.02030.125-0.12490.35390.1252-0.36010.21050.35550.01250.01040.7618-0.060.334811.190824.127921.712
22.51160.2797-0.11971.70651.54983.9699-0.0104-0.10170.2545-0.1543-0.04010.1328-0.4476-0.08210.01670.35510.02710.04920.59310.02540.282215.82118.21091.6753
32.20340.54430.22961.90980.14493.36020.13840.07030.0199-0.2883-0.05620.14280.0243-0.46410.0030.32750.01120.00960.49680.03730.179518.569411.9178-4.5098
46.4063-4.54752.31536.9297-1.41845.2644-0.3463-0.62990.57550.63580.387-0.3727-0.05390.0543-0.12180.3853-0.0120.07350.452-0.08490.254326.564120.249216.0082
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 79 )
2X-RAY DIFFRACTION2chain 'A' and (resid 80 through 150 )
3X-RAY DIFFRACTION3chain 'A' and (resid 151 through 238 )
4X-RAY DIFFRACTION4chain 'A' and (resid 239 through 264 )

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