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- PDB-6gzo: Crystal structure of NadR protein in complex with NAD and AMP-PNP -

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Basic information

Entry
Database: PDB / ID: 6gzo
TitleCrystal structure of NadR protein in complex with NAD and AMP-PNP
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHATE ION / 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: 3 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
DepositionJul 4, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 5, 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)90,6717
Polymers88,2362
Non-polymers2,4345
Water00
1
A: Nicotinamide-nucleotide adenylyltransferase NadR family / Ribosylnicotinamide kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3834
Polymers44,1181
Non-polymers1,2653
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)45,2883
Polymers44,1181
Non-polymers1,1702
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)167.320, 167.320, 192.810
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-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4

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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: 4.41 Å3/Da / Density % sol: 72.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1M (NH4)2SO4, 100mM Na Citrate, 10mM MgCl2, 0% 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: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3→47 Å / Num. obs: 32450 / % possible obs: 99.9 % / Redundancy: 8 % / Net I/σ(I): 9
Reflection shellResolution: 3→3.1 Å / Num. unique obs: 2510 / % possible all: 99.9

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Processing

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

6gyf


Resolution: 3→45.738 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.33
RfactorNum. reflection% reflection
Rfree0.24 1623 5 %
Rwork0.19 --
obs0.1925 32439 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3→45.738 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5811 0 155 0 5966
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096138
X-RAY DIFFRACTIONf_angle_d1.2758336
X-RAY DIFFRACTIONf_dihedral_angle_d19.1423643
X-RAY DIFFRACTIONf_chiral_restr0.063887
X-RAY DIFFRACTIONf_plane_restr0.0071076
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.08820.37121320.36322510X-RAY DIFFRACTION100
3.0882-3.18790.39161320.3452510X-RAY DIFFRACTION100
3.1879-3.30180.35171330.31972525X-RAY DIFFRACTION100
3.3018-3.4340.37841330.28462516X-RAY DIFFRACTION100
3.434-3.59020.3351330.24112536X-RAY DIFFRACTION100
3.5902-3.77940.27531340.21122540X-RAY DIFFRACTION100
3.7794-4.01610.22511340.17582544X-RAY DIFFRACTION100
4.0161-4.32590.22191340.15462545X-RAY DIFFRACTION100
4.3259-4.76080.16891350.13152577X-RAY DIFFRACTION100
4.7608-5.44880.20731370.1512593X-RAY DIFFRACTION100
5.4488-6.86120.20351380.20682631X-RAY DIFFRACTION100
6.8612-45.74350.241480.17342789X-RAY DIFFRACTION100
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)
12.81590.2103-1.24684.8448-0.34154.50210.2596-0.24660.27970.9704-0.10540.0118-0.22550.7459-0.19710.6762-0.0714-0.16450.7839-0.22540.619615.466377.032517.1599
24.5886-1.8555-0.42096.26240.34834.62540.17470.11570.4547-0.54290.1466-0.6934-0.80490.1816-0.29460.851-0.1724-0.09010.7085-0.04610.712424.810678.566912.1826
33.42873.2616-1.0674.3196-3.83127.4943-0.4182-1.47891.77870.26210.8408-0.9997-1.30740.2373-0.22710.9961-0.22170.03490.8881-0.28691.436926.106688.202422.1492
42.3375-0.6131-2.68253.10231.6183.5103-0.01350.3791-0.6436-0.58120.0078-0.19391.55730.0644-0.05620.89360.0252-0.24840.83850.00940.93520.959760.241721.112
52.2686-0.24270.49460.642-0.58739.67990.42290.5781-0.7154-0.5404-0.1742-0.0811-0.2116-1.4748-0.31370.8378-0.0234-0.30040.9086-0.09460.867213.69837.02262.1108
62.79740.1055-1.28311.33640.43416.04090.17680.4011-0.4237-0.29370.1032-0.44020.5320.5702-0.2350.88520.0327-0.26830.8895-0.0750.911323.898138.2375-0.0579
77.91492.5368-5.31322.66111.41948.8106-0.2185-1.87220.06971.6021-0.0821-0.59290.56861.11750.30621.12850.1631-0.37441.05290.06671.075120.751635.963621.8846
84.5911-0.4561.35965.77341.29194.1009-0.0704-0.2759-0.60771.61720.3935-0.66710.8401-0.1105-0.35880.8712-0.1229-0.31810.93740.25270.94065.457529.965223.358
93.78350.58750.28327.9845-0.73812.93740.1818-0.2466-0.72950.19770.17890.34270.6903-0.3819-0.3141.06-0.2363-0.35120.98620.22830.8416-1.446230.812728.9664
105.4189-1.44543.02322.0463-0.7933.48590.24350.6337-0.2452-0.35560.07610.41870.217-0.332-0.29550.7631-0.0208-0.15210.99560.09240.6964-9.492366.934113.3913
119.470.5823-0.49693.6294-0.15572.6075-0.3314-0.81110.50730.270.42180.6062-0.5277-0.897-0.05440.91410.0983-0.00321.00480.01490.66-10.024471.607323.9864
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 40 )
2X-RAY DIFFRACTION2chain 'A' and (resid 41 through 125 )
3X-RAY DIFFRACTION3chain 'A' and (resid 126 through 150 )
4X-RAY DIFFRACTION4chain 'A' and (resid 151 through 179 )
5X-RAY DIFFRACTION5chain 'A' and (resid 180 through 228 )
6X-RAY DIFFRACTION6chain 'A' and (resid 229 through 355 )
7X-RAY DIFFRACTION7chain 'A' and (resid 356 through 375 )
8X-RAY DIFFRACTION8chain 'B' and (resid 9 through 40 )
9X-RAY DIFFRACTION9chain 'B' and (resid 41 through 179 )
10X-RAY DIFFRACTION10chain 'B' and (resid 180 through 274 )
11X-RAY DIFFRACTION11chain 'B' and (resid 275 through 377 )

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