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

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Basic information

Entry
Database: PDB / ID: 6rge
TitleCrystal structure of NAD kinase 1 from Listeria monocytogenes in complex with an inhibitor
ComponentsNAD kinase 1
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 / Chem-K1Z / NAD kinase 1
Similarity search - Component
Biological speciesListeria monocytogenes EGD-e (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.801 Å
AuthorsGelin, M. / Labesse, G.
CitationJournal: To Be Published
Title: Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with an inhibitor
Authors: Gelin, M. / Labesse, G.
History
DepositionApr 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1May 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)31,8883
Polymers31,0451
Non-polymers8432
Water1,33374
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)127,55212
Polymers124,1814
Non-polymers3,3708
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)63.080, 75.220, 118.280
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-421-

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 / Gene: nadK1, lmo0968 / Variant: ATCC BAA-679 / EGD-e / 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-K1Z / [(2~{R},3~{R},4~{R},5~{R})-2-[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]-5-(hydroxymethyl)-4-oxidanyl-oxolan-3-yl] dihydrogen phosphate


Mass: 650.495 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H27N10O11P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 45.57 %
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: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Oct 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.799→59.14 Å / Num. obs: 25981 / % possible obs: 98 % / Redundancy: 3.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.02 / Rrim(I) all: 0.042 / Net I/σ(I): 16.2 / Num. measured all: 101054
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
1.799-1.833.90.472491812540.9020.2670.5462.195.7
4.883-59.1440.022549513630.9990.0120.02545.494.7

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.801→59.14 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2228 1028 4.8 %
Rwork0.2006 20385 -
obs0.2016 21413 80.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.67 Å2 / Biso mean: 33.6674 Å2 / Biso min: 10.26 Å2
Refinement stepCycle: final / Resolution: 1.801→59.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2048 0 58 74 2180
Biso mean--26.47 31.3 -
Num. residues----259
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8011-1.8960.2302320.23959162317
1.896-2.01480.25571080.24622274238264
2.0148-2.17040.30391820.23023410359296
2.1704-2.38880.25861580.22693561371999
2.3888-2.73450.20011850.2063543372899
2.7345-3.44510.20931800.2013374355494
3.4451-59.17190.20611830.17663632381596
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)
14.1718-1.369-2.25271.3870.99394.9493-0.1531-0.3180.19420.22610.03410.0375-0.3311-0.31370.08160.36720.0920.05270.3116-0.10480.253711.867423.29921.9907
22.1836-0.4068-1.08842.52560.85795.88670.0874-0.24930.5790.0323-0.07650.0231-0.9381-0.21990.02380.28530.16550.04840.2646-0.03680.374116.439325.709412.7623
31.7048-0.63360.09392.4031.38968.93510.09060.0873-0.1771-0.016-0.17140.44860.6634-0.79060.09050.14270.0128-0.03970.2624-0.01770.269414.6558.3993-7.2996
41.40210.46530.58611.64050.65424.32860.00690.03610.1101-0.0648-0.02450.1227-0.1397-0.1080.01590.11880.03440.00150.1385-0.00230.153223.350511.8154-1.9955
53.3524-0.14030.54513.9675-0.10074.40690.03620.3498-0.0918-0.3613-0.0670.63750.2409-0.3010.03640.18510.0271-0.020.22940.00990.203220.57339.4065-11.2692
62.3311-0.11730.87844.21370.40966.4659-0.01140.0273-0.0001-0.2002-0.16120.90390.1369-1.6790.07640.19160.0875-0.01420.5048-0.0380.43969.198613.7245-4.1276
78.199-3.49652.32165.4742-0.67861.7647-0.3128-1.0651.06450.20060.1667-0.4838-0.7786-0.47060.17420.38710.03760.04960.2722-0.12550.346423.265926.61315.0783
87.1738-0.6117-0.25292.70022.73397.28890.0542-0.79920.01030.73490.022-0.2981-0.21620.17120.04240.24280.00690.00750.2248-0.05140.194531.732712.827217.5724
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 79 )A1 - 79
2X-RAY DIFFRACTION2chain 'A' and (resid 80 through 120 )A80 - 120
3X-RAY DIFFRACTION3chain 'A' and (resid 121 through 141 )A121 - 141
4X-RAY DIFFRACTION4chain 'A' and (resid 142 through 184 )A142 - 184
5X-RAY DIFFRACTION5chain 'A' and (resid 185 through 216 )A185 - 216
6X-RAY DIFFRACTION6chain 'A' and (resid 217 through 238 )A217 - 238
7X-RAY DIFFRACTION7chain 'A' and (resid 239 through 252 )A239 - 252
8X-RAY DIFFRACTION8chain 'A' and (resid 253 through 264 )A253 - 264

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