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- PDB-6rc6: Crystal structure of NAD kinase 1 from Listeria monocytogenes in ... -

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Basic information

Entry
Database: PDB / ID: 6rc6
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 / Chem-JY5 / NAD kinase 1
Similarity search - Component
Biological speciesListeria monocytogenes serovar 1/2a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 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)31,5113
Polymers31,0451
Non-polymers4652
Water1,53185
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)126,04312
Polymers124,1814
Non-polymers1,8628
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 area9680 Å2
ΔGint-48 kcal/mol
Surface area42140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.610, 75.430, 118.340
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Components on special symmetry positions
IDModelComponents
11A-414-

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 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


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-JY5 / 3-[6-azanyl-9-[(2~{R})-oxan-2-yl]purin-8-yl]prop-2-yn-1-ol


Mass: 273.291 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H15N5O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 45.34 % / Mosaicity: 1.48 °
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: ID14-4 / Wavelength: 0.939274 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 26, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939274 Å / Relative weight: 1
ReflectionResolution: 2.29→55.34 Å / Num. obs: 11859 / % possible obs: 91.9 % / Redundancy: 5.7 % / Biso Wilson estimate: 36.22 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.034 / Rrim(I) all: 0.082 / Net I/σ(I): 15.8 / Num. measured all: 67758 / Scaling rejects: 152
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
2.29-2.375.90.584721612250.9420.2540.639498.6
8.87-55.345.20.0312362400.9990.0150.03332.693.5

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PHENIX1.14_3260refinement
MOSFLMdata reduction
Aimless0.7.1data scaling
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.29→34.96 Å / SU ML: 0.2725 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.1918 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2278 570 4.82 %
Rwork0.1889 11263 -
obs0.1907 11833 91.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.43 Å2
Refinement stepCycle: LAST / Resolution: 2.29→34.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2068 0 33 85 2186
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032171
X-RAY DIFFRACTIONf_angle_d0.61442939
X-RAY DIFFRACTIONf_chiral_restr0.0465317
X-RAY DIFFRACTIONf_plane_restr0.0031375
X-RAY DIFFRACTIONf_dihedral_angle_d19.62341278
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.520.26791610.22742961X-RAY DIFFRACTION97.68
2.52-2.890.26091440.22162632X-RAY DIFFRACTION87.08
2.89-3.630.22041370.19982861X-RAY DIFFRACTION92.65
3.63-34.960.20911280.16412809X-RAY DIFFRACTION92.36
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)
11.51207934999-0.662464235132-1.269863359830.7845079192111.27345646173.97886302064-0.0295501055632-0.2642025340820.1396328618380.02311655481820.02367618674560.133436630348-0.288275047937-0.1760510276730.02051337954350.3537018416110.06140335215580.01949159611690.359494156698-0.01649079581930.36305402406912.620180026921.738637044114.5154537909
21.54640815297-0.329820383192-0.003033135603792.001712417620.1783979835423.34163496574-0.002693931269980.16435648660.0376746393168-0.0663276599130.01778296560870.1359017396970.123541049151-0.1454006960290.02964362051180.1844622388250.01114558259930.002777979805340.2419962573450.01130595004170.25829450076422.188112567711.0460326527-5.97956611296
31.82354748189-0.3491685458180.3872378075831.769172177140.3530890872133.56987907366-0.00186010708946-0.2176716882030.19748553330.0686494604072-0.01278013488280.266184590179-0.191867485098-0.3065364994690.03406275097340.2320405265210.02017014361830.05941893480340.261245186477-0.01208652217550.34596657680718.814748640316.92398454286.97251798988
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 141 )
2X-RAY DIFFRACTION2chain 'A' and (resid 142 through 216 )
3X-RAY DIFFRACTION3chain 'A' and (resid 217 through 264 )

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