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- PDB-6gyf: Crystal structure of NadR protein in complex with NR -

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Basic information

Entry
Database: PDB / ID: 6gyf
TitleCrystal structure of NadR protein in complex with NR
ComponentsNicotinamide-nucleotide adenylyltransferase NadR family / Ribosylnicotinamide kinase
KeywordsTRANSPORT PROTEIN / vitamin transport / phosphorylation / NAD+ / NadR
Function / homology
Function and homology information


ribosylnicotinamide kinase activity / nicotinamide-nucleotide adenylyltransferase activity / NAD biosynthetic process
Similarity search - Function
Nicotinamide-nucleotide adenylyltransferase / NAD biosynthesis/regulator protein NadR / NadR/Ttd14, AAA domain / NadR, nicotinamide/nicotinate mononucleotide adenylyltransferase domain / AAA domain / Cytidyltransferase-like domain / Rossmann-like alpha/beta/alpha sandwich fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE / Nicotinamide-nucleotide adenylyltransferase NadR family / Ribosylnicotinamide kinase
Similarity search - Component
Biological speciesLactococcus lactis subsp. cremoris (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSingh, R. / Stetsenko, A. / Jaehme, M. / Guskov, A. / Slotboom, D.J.
CitationJournal: Molecules / Year: 2020
Title: Structural and Functional Characterization of NadR fromLactococcus lactis.
Authors: Stetsenko, A. / Singh, R. / Jaehme, M. / Guskov, A. / Slotboom, D.J.
History
DepositionJun 29, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 17, 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

Downloads & links

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Assembly

Deposited unit
A: Nicotinamide-nucleotide adenylyltransferase NadR family / Ribosylnicotinamide kinase
B: Nicotinamide-nucleotide adenylyltransferase NadR family / Ribosylnicotinamide kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,36411
Polymers88,2362
Non-polymers1,1289
Water00
1
A: Nicotinamide-nucleotide adenylyltransferase NadR family / Ribosylnicotinamide kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6946
Polymers44,1181
Non-polymers5765
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nicotinamide-nucleotide adenylyltransferase NadR family / Ribosylnicotinamide kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6705
Polymers44,1181
Non-polymers5524
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)165.090, 165.090, 193.050
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein Nicotinamide-nucleotide adenylyltransferase NadR family / Ribosylnicotinamide kinase


Mass: 44118.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis subsp. cremoris (lactic acid bacteria)
Gene: NCDO763_1675 / Production host: Escherichia coli MC1061 (bacteria) / References: UniProt: A0A165F602
#2: Chemical ChemComp-NMN / BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE / NICOTINAMIDE MONONUCLEOTIDE


Mass: 335.227 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H16N2O8P
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg

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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: 4.3 Å3/Da / Density % sol: 71.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1M (NH4)2SO4, 100mM Na Citrate pH 6.5, 10mM MgCl2 and 10% glucose

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.7→47.827 Å / Num. obs: 41587 / % possible obs: 96 % / Redundancy: 11 % / Net I/σ(I): 10
Reflection shellResolution: 2.7→2.8 Å

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Processing

Software
NameVersionClassification
PHENIX(dev_3150)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GYE

6gye


Resolution: 2.7→47.827 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.41
RfactorNum. reflection% reflection
Rfree0.2388 2080 5 %
Rwork0.1975 --
obs0.1996 41577 96.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→47.827 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5937 0 67 0 6004
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096245
X-RAY DIFFRACTIONf_angle_d1.0548472
X-RAY DIFFRACTIONf_dihedral_angle_d19.0673713
X-RAY DIFFRACTIONf_chiral_restr0.057897
X-RAY DIFFRACTIONf_plane_restr0.0061121
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7002-2.7630.40591360.41612582X-RAY DIFFRACTION96
2.763-2.83210.3931370.38712603X-RAY DIFFRACTION98
2.8321-2.90870.37911370.34142608X-RAY DIFFRACTION98
2.9087-2.99420.35531390.31962628X-RAY DIFFRACTION98
2.9942-3.09090.37261370.29992616X-RAY DIFFRACTION97
3.0909-3.20130.32881380.29452617X-RAY DIFFRACTION97
3.2013-3.32950.36371380.27522610X-RAY DIFFRACTION96
3.3295-3.4810.31181380.2252634X-RAY DIFFRACTION97
3.481-3.66440.23661380.20272627X-RAY DIFFRACTION97
3.6644-3.89390.23361380.17172617X-RAY DIFFRACTION97
3.8939-4.19440.19161390.1492631X-RAY DIFFRACTION96
4.1944-4.61620.17171390.12982644X-RAY DIFFRACTION96
4.6162-5.28340.19531380.13532633X-RAY DIFFRACTION95
5.2834-6.65370.21991410.18042676X-RAY DIFFRACTION95
6.6537-47.83430.18851470.17282771X-RAY DIFFRACTION93
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)
11.1641-1.16060.42063.4286-0.55630.88740.1497-0.2323-0.36150.21980.08190.31140.2551-0.2824-0.26250.677-0.1537-0.15490.77480.0990.5819-5.064544.033222.0341
27.13780.19130.73332.3082-0.27671.9434-0.1963-0.98850.70040.30370.0636-0.0383-0.4267-0.54870.16750.73620.03710.00990.745-0.14980.4718-6.156773.528524.2982
33.5097-0.7939-2.64965.24242.46333.09440.03630.02610.1127-0.28030.03180.0359-0.0289-0.0747-0.03880.4441-0.0248-0.16030.4925-0.00850.438819.979872.530614.2148
47.93482.9451-0.36027.06542.97185.00760.089-0.62580.5436-0.3334-0.064-0.2792-0.20830.0064-0.05130.54690.0225-0.04990.40060.02360.31925.500976.489811.8117
55.58490.4705-0.08865.78160.90875.33070.0381-0.19970.9967-0.52070.067-0.1758-0.0762-0.0303-0.09990.6543-0.05160.00310.4148-0.10990.615324.80986.330817.2606
68.26970.6278-0.72362.65961.53916.6473-0.1255-0.5055-0.37090.360.4575-0.27650.81340.3326-0.31150.74760.008-0.05410.6032-0.03360.528120.706359.075420.7771
74.7793-0.1256-1.75794.5329-0.39913.32-0.03580.4396-0.5607-0.15880.1910.36810.649-0.0391-0.23480.68290.0058-0.26390.5778-0.00090.562915.394735.757710.504
80.39040.74481.69822.6054.4358.2210.38770.1779-0.76330.1953-0.1318-0.0291.1766-0.0197-0.17860.8170.0976-0.25840.8398-0.14990.640411.463636.3821-5.076
93.4619-0.8594-1.89852.92781.05915.97880.1260.3913-0.34430.04430.021-0.33390.52290.214-0.17220.50870.058-0.17220.6465-0.04930.556123.375137.5652-1.0349
103.03142.8037-0.76033.0067-0.90689.7391-0.4163-0.6476-0.36591.11690.4927-1.04690.23290.5066-0.06980.90530.078-0.41520.80150.06130.905221.9930.48920.4182
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 290 )
2X-RAY DIFFRACTION2chain 'A' and (resid 291 through 379 )
3X-RAY DIFFRACTION3chain 'B' and (resid 8 through 73 )
4X-RAY DIFFRACTION4chain 'B' and (resid 74 through 96 )
5X-RAY DIFFRACTION5chain 'B' and (resid 97 through 150 )
6X-RAY DIFFRACTION6chain 'B' and (resid 151 through 179 )
7X-RAY DIFFRACTION7chain 'B' and (resid 180 through 204 )
8X-RAY DIFFRACTION8chain 'B' and (resid 205 through 228 )
9X-RAY DIFFRACTION9chain 'B' and (resid 229 through 342 )
10X-RAY DIFFRACTION10chain 'B' and (resid 343 through 378 )

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