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

ID or keywords:

Entry

Database: PDB / ID: 6gye

Title

Crystal structure of NadR protein in complex with NR

Components

Nicotinamide-nucleotide adenylyltransferase NadR family / Ribosylnicotinamide kinase

Keywords

TRANSPORT 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

Biological species

Lactococcus lactis subsp. cremoris (lactic acid bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Singh, R. / Stetsenko, A. / Jaehme, M. / Guskov, A. / Slotboom, D.J.

Citation

Journal: 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

Deposition	Jun 29, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 10, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jul 22, 2020	Group: 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 1.2	Jan 17, 2024	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6gye.cif.gz	324 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gy/6gye ftp://data.pdbj.org/pub/pdb/validation_reports/gy/6gye	HTTPS FTP

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Related structure data

Related structure data	6gyfC 6gzoC 1lw7S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6gyf-2 6gzo-2 4dmy-d 6gzo-1 3ajh-d 4ct5-1 5cve-d 1wnx-d 1gml-2 3i0u-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Nicotinamide-nucleotide adenylyltransferase NadR family / Ribosylnicotinamide kinase

B: Nicotinamide-nucleotide adenylyltransferase NadR family / Ribosylnicotinamide kinase

hetero molecules

89.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Nicotinamide-nucleotide adenylyltransferase NadR family / Ribosylnicotinamide kinase

hetero molecules

defined by author
Evidence: light scattering, monomeric peak
44.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Nicotinamide-nucleotide adenylyltransferase NadR family / Ribosylnicotinamide kinase

hetero molecules

defined by author
44.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	165.140, 165.140, 196.550
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	181
Space group name H-M	P6₄22

#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-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-NNR / Nicotinamide riboside / 3-(aminocarbonyl)-1-beta-D-ribofuranosylpyridinium / Nicotinamide riboside Mass: 255.247 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Formula: C₁₁H₁₅N₂O₅
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 4.38 Å³/Da / Density % sol: 71.94 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1M (NH4)2SO4, 100mM Na Citrate, 10mM MgCl2 and 10% glucose

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.87 Å
Detector	Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 30, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.87 Å / Relative weight: 1
Reflection	Resolution: 2.3→47.37 Å / Num. obs: 70447 / % possible obs: 100 % / Redundancy: 13.5 % / R_merge(I) obs: 0.16 / Net I/av σ(I): 12.47 / Net I/σ(I): 10.99
Reflection shell	Resolution: 2.3→2.4 Å / Redundancy: 13.4 % / R_merge(I) obs: 2.98 / Mean I/σ(I) obs: 0.87 / Num. unique obs: 8304 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(dev_3150: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1LW7

1lw7

Resolution: 2.3→47.363 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.74

	R_factor	Num. reflection	% reflection
R_free	0.2132	3522	5 %
R_work	0.1801	-	-
obs	0.1817	70441	99.98 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.3→47.363 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5944	0	96	266	6306

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	6318
X-RAY DIFFRACTION	f_angle_d	0.958	8575
X-RAY DIFFRACTION	f_dihedral_angle_d	16.655	3754
X-RAY DIFFRACTION	f_chiral_restr	0.057	900
X-RAY DIFFRACTION	f_plane_restr	0.006	1132

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.3-2.3315	0.3795	139	0.3449	2630	X-RAY DIFFRACTION	100
2.3315-2.3648	0.3308	137	0.333	2612	X-RAY DIFFRACTION	100
2.3648-2.4001	0.2963	140	0.31	2661	X-RAY DIFFRACTION	100
2.4001-2.4376	0.3322	138	0.3036	2613	X-RAY DIFFRACTION	100
2.4376-2.4776	0.2942	139	0.2691	2647	X-RAY DIFFRACTION	100
2.4776-2.5203	0.2762	139	0.2733	2647	X-RAY DIFFRACTION	100
2.5203-2.5662	0.313	139	0.2653	2623	X-RAY DIFFRACTION	100
2.5662-2.6155	0.2893	139	0.2542	2653	X-RAY DIFFRACTION	100
2.6155-2.6689	0.285	139	0.246	2644	X-RAY DIFFRACTION	100
2.6689-2.7269	0.3011	138	0.2368	2622	X-RAY DIFFRACTION	100
2.7269-2.7903	0.2694	140	0.2265	2659	X-RAY DIFFRACTION	100
2.7903-2.8601	0.2543	140	0.2068	2655	X-RAY DIFFRACTION	100
2.8601-2.9374	0.2398	139	0.1991	2645	X-RAY DIFFRACTION	100
2.9374-3.0239	0.2456	140	0.186	2658	X-RAY DIFFRACTION	100
3.0239-3.1214	0.2	140	0.1814	2666	X-RAY DIFFRACTION	100
3.1214-3.233	0.2653	140	0.1769	2659	X-RAY DIFFRACTION	100
3.233-3.3624	0.2107	141	0.1741	2666	X-RAY DIFFRACTION	100
3.3624-3.5154	0.1933	141	0.1583	2685	X-RAY DIFFRACTION	100
3.5154-3.7006	0.1861	141	0.1543	2674	X-RAY DIFFRACTION	100
3.7006-3.9324	0.1871	142	0.1431	2709	X-RAY DIFFRACTION	100
3.9324-4.2358	0.1604	142	0.1386	2699	X-RAY DIFFRACTION	100
4.2358-4.6618	0.1675	143	0.1261	2709	X-RAY DIFFRACTION	100
4.6618-5.3355	0.1667	145	0.1466	2761	X-RAY DIFFRACTION	100
5.3355-6.7192	0.2122	146	0.1907	2759	X-RAY DIFFRACTION	100
6.7192-47.3729	0.2102	155	0.1888	2963	X-RAY DIFFRACTION	100

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	1.2783	-0.4902	0.5148	4.6982	-1.3451	0.9201	0.2269	-0.3135	-0.5019	0.2621	0.0827	0.2285	0.2696	-0.3034	-0.3092	0.6327	-0.1835	-0.218	0.6654	0.1425	0.5218	-1.0003	34.1448	27.2287
2	2.5644	-1.5028	2.152	1.71	-0.908	3.0032	0.0519	-0.2578	0.0126	-0.0761	0.103	0.2148	-0.0405	-0.5101	-0.1564	0.4406	-0.0306	-0.0595	0.6146	0.0575	0.4468	-12.3384	64.9442	11.2048
3	3.9215	0.9988	1.2535	2.3888	0.7258	3.4908	-0.0236	-0.7724	0.5682	0.1431	-0.0062	0.3394	-0.3249	-0.8101	0.0832	0.5033	0.0381	0.0504	0.7163	-0.0195	0.4519	-10.4215	70.9704	23.5527
4	0.8151	0.6248	0.1601	3.6576	1.0213	1.4262	0.0677	-0.0434	0.1078	-0.0925	0.0981	-0.0965	-0.1253	0.1117	-0.1755	0.4011	-0.0123	-0.0911	0.5003	-0.0336	0.4324	21.5886	70.765	15.7837
5	1.407	-0.2751	0.5273	1.6204	1.5524	4.135	0.2683	0.3974	-0.3333	-0.1904	-0.1239	0.0436	0.192	0.1123	-0.0621	0.5638	0.0493	-0.1938	0.5235	-0.0509	0.4831	16.2838	39.7061	-2.6767
6	3.0158	-1.2359	-1.6144	3.676	-0.5713	7.3809	0.1198	0.3713	-0.2976	-0.0535	0.0088	-0.2412	0.8228	0.7158	-0.0233	0.4409	0.1195	-0.1792	0.6308	-0.0668	0.5974	26.7651	34.5501	-1.1311
7	8.9458	1.1421	-3.0662	4.3472	1.2975	2.1586	-0.4384	-0.6759	-1.1099	0.7605	-0.0201	-0.6208	0.2073	0.6346	0.0287	0.8377	0.0118	-0.4291	0.74	0.1432	0.7919	22.6049	29.5482	20.4409

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 8 through 204 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 205 through 274 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 275 through 379 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 8 through 204 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 205 through 274 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 275 through 342 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 343 through 378 )

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