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

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Basic information

Entry
Database: PDB / ID: 6rbx
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 / 3-(6-azanyl-8-bromanyl-purin-9-yl)propan-1-ol / NAD kinase 1
Similarity search - Component
Biological speciesListeria monocytogenes EGD-e (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 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)31,5103
Polymers31,0451
Non-polymers4642
Water1,44180
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)126,03812
Polymers124,1814
Non-polymers1,8578
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)63.340, 75.710, 119.450
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 EGD-e (bacteria)
Gene: nadK1, lmo0968 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8Y8D7, NAD+ kinase
#2: Chemical ChemComp-JYT / 3-(6-azanyl-8-bromanyl-purin-9-yl)propan-1-ol


Mass: 272.102 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10BrN5O
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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 %
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: ID29 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 9, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.46→59.761 Å / Num. all: 10620 / Num. obs: 10620 / % possible obs: 99 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.055 / Rrim(I) all: 0.101 / Rsym value: 0.082 / Net I/av σ(I): 6 / Net I/σ(I): 8.4 / Num. measured all: 36785
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.46-2.594.30.5021.5653915320.3170.6720.5021.299.7
2.59-2.754.20.3472.2608414650.2220.4630.3471.899.5
2.75-2.9440.2593539113540.170.3470.2592.399.5
2.94-3.183.80.155.1480012760.1040.2040.15499.5
3.18-3.483.40.0957.5398611790.0680.1250.0956.499.5
3.48-3.892.90.04814.1315210810.0390.0650.04811.199.3
3.89-4.492.70.0319.225499410.0280.0440.031698.6
4.49-5.52.30.02616.818397900.0270.040.02620.296
5.5-7.782.50.02123.716096310.0190.030.02123.797.6
7.78-63.9452.30.0359.18363710.0320.0470.03529.297.6

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
MOSFLMdata reduction
SCALA3.2.19data scaling
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.47→59.725 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.73
RfactorNum. reflection% reflection
Rfree0.2589 823 10.01 %
Rwork0.2136 --
obs0.2182 8225 77.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 143.17 Å2 / Biso mean: 45.7294 Å2 / Biso min: 19.38 Å2
Refinement stepCycle: final / Resolution: 2.47→59.725 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2064 0 28 80 2172
Biso mean--46.71 43.69 -
Num. residues----261
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4701-2.62490.2951240.255821924314
2.6249-2.82750.2841010.2784912101358
2.8275-3.11210.31351680.27851508167695
3.1121-3.56240.30981750.231570174599
3.5624-4.4880.23251750.17681578175398
4.488-59.74240.2281800.20181615179596
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)
11.9504-0.297-0.89490.58630.12021.78950.0508-0.4660.1478-0.01860.04410.2136-0.3195-0.0095-0.0930.38290.07240.08090.426-0.12830.345911.609323.649222.152
20.6353-0.0544-1.14610.1290.53193.48680.0494-0.49970.40870.07740.2951-0.0555-0.58170.5017-0.15910.56-0.01650.07530.5227-0.25170.511520.638528.733723.412
32.0560.0266-0.24292.0593-0.49922.44250.1250.19290.1103-0.1778-0.10130.3614-0.1257-0.2897-0.00720.19790.0639-0.01490.2908-0.01630.25919.263612.0487-6.1784
41.3257-0.224-0.80141.5006-0.01511.3240.0419-0.07490.5160.1235-0.10590.4565-0.3069-0.187-0.06350.31810.02870.05450.2078-0.04690.373319.065617.08147.199
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 102 )A80 - 102
3X-RAY DIFFRACTION3chain 'A' and (resid 103 through 216 )A103 - 216
4X-RAY DIFFRACTION4chain 'A' and (resid 217 through 264 )A217 - 264

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