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- PDB-6z64: Crystal structure of NAD kinase 1 from Listeria monocytogenes in ... -

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Basic information

Entry
Database: PDB / ID: 6z64
TitleCrystal structure of NAD kinase 1 from Listeria monocytogenes in complex with a di-adenosine 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
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
Similarity search - Domain/homology
CITRIC ACID / Chem-Q9K / NAD kinase 1
Similarity search - Component
Biological speciesListeria monocytogenes EGD-e (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsGelin, M. / Labesse, G.
CitationJournal: Molecules / Year: 2020
Title: New Chemical Probe Targeting Bacterial NAD Kinase.
Authors: Clement, D.A. / Leseigneur, C. / Gelin, M. / Coelho, D. / Huteau, V. / Lionne, C. / Labesse, G. / Dussurget, O. / Pochet, S.
History
DepositionMay 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)31,8643
Polymers31,0451
Non-polymers8192
Water1,11762
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)127,45612
Polymers124,1814
Non-polymers3,2758
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)62.846, 74.170, 118.392
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-419-

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 BL21(DE3) (bacteria) / 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-Q9K / (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-[[3-[6-azanyl-9-[(2~{R},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]purin-8-yl]prop-2-ynyl-(3-azanylpropyl)amino]methyl]oxolane-3,4-diol


Mass: 626.624 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H34N12O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.22 Å3/Da / Density % sol: 44.64 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 30 mM NaBr, 220 mM Kcitrate, glycerol 6%, 15-16% w/v PEG400
PH range: 4.8-5.1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.89→47.95 Å / Num. obs: 22467 / % possible obs: 99.5 % / Redundancy: 5.326 % / Biso Wilson estimate: 47.081 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rrim(I) all: 0.061 / Χ2: 1.08 / Net I/σ(I): 14.06 / Num. measured all: 119667
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.89-2.025.5671.3681.3122440404240310.6941.51199.7
2.02-2.185.270.6962.5519482371436970.9070.77499.5
2.18-2.385.5110.3665.0318512336733590.9710.40699.8
2.38-2.665.20.1858.8316426317931590.9920.20799.4
2.66-3.075.3950.09115.8215273284328310.9970.10299.6
3.07-3.765.0680.04230.0812174241324020.9980.04799.5
3.76-5.35.1470.02945.259630188918710.9990.03299
5.3-47.955.130.01948.8757301129111710.02198.9

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RG9

6rg9


Resolution: 1.89→47.95 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2361 2064 9.22 %
Rwork0.205 20318 -
obs0.2078 22382 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 121.82 Å2 / Biso mean: 54.33 Å2 / Biso min: 28.65 Å2
Refinement stepCycle: final / Resolution: 1.89→47.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2078 0 58 62 2198
Biso mean--47.79 50.92 -
Num. residues----262
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.89-1.930.41281380.39621296143498
1.93-1.980.38831230.353113731496100
1.98-2.040.35531320.31911325145799
2.04-2.10.32431240.28271364148899
2.1-2.160.29591300.27461331146199
2.16-2.240.2961450.23531341148699
2.24-2.330.2531260.224713521478100
2.33-2.440.28151330.2081342147599
2.44-2.560.2551480.20281341148999
2.57-2.730.22391550.20271324147999
2.73-2.940.24641460.226213521498100
2.94-3.230.27191290.20511369149899
3.23-3.70.2131460.180213621508100
3.7-4.660.17321450.16171386153199
4.66-47.950.23611440.20231460160499
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)
14.2807-0.7491-3.12971.50340.31046.3450.0471-0.45280.31950.13450.0331-0.0712-0.30890.0989-0.00960.51280.04660.03610.5078-0.12290.447213.637524.329422.3966
21.4670.18130.52022.52180.70823.97410.06790.09330.0413-0.1804-0.14830.4097-0.0283-0.64540.02310.29750.0505-0.01680.4528-0.01160.386215.596611.6492-5.8432
31.5139-0.66770.16112.5881-0.0833.6080.1032-0.01130.1258-0.0128-0.17530.3468-0.0655-0.33850.04640.26420.0160.02350.3368-0.01870.380120.816214.18950.4704
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 102 )A1 - 102
2X-RAY DIFFRACTION2chain 'A' and (resid 103 through 166 )A103 - 166
3X-RAY DIFFRACTION3chain 'A' and (resid 167 through 264 )A167 - 264

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