PDB-5dhq: Crystal structure of NAD kinase 1 from Listeria monocytogenes in ...

ID or keywords:

Entry

Database: PDB / ID: 5dhq

Title

Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with a novel inhibitor

Components

NAD kinase 1

Keywords

TRANSFERASE / 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

Biological species

Listeria monocytogenes serovar 1/2a (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.29 Å

Authors

Gelin, M. / Paoletti, J. / Assairi, L. / Huteau, V. / Pochet, S. / Labesse, G.

Funding support

France, 1items

Citation

Journal: Eur.J.Med.Chem. / Year: 2016
Title: 8-Thioalkyl-adenosine derivatives inhibit Listeria monocytogenes NAD kinase through a novel binding mode.
Authors: Paoletti, J. / Assairi, L. / Gelin, M. / Huteau, V. / Nahori, M.A. / Dussurget, O. / Labesse, G. / Pochet, S.

History

Deposition	Aug 31, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Sep 14, 2016	Provider: repository / Type: Initial release
Revision 1.1	Nov 9, 2016	Group: Database references
Revision 1.2	Sep 6, 2017	Group: Author supporting evidence / Data collection / Category: diffrn_radiation_wavelength / pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Jan 10, 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	5dhq.cif.gz	431.8 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dh/5dhq ftp://data.pdbj.org/pub/pdb/validation_reports/dh/5dhq	HTTPS FTP

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Related structure data

Related structure data	5dhpC 5dhrC 5dhsC 5dhtC 5dhuC 2i1wS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5dht-d 6rc2-1 6rbw-1 6rg6-1 2i2f-1 6rbo-1 6rbx-1 5dhu-d 6rbv-1 5dhs-d 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: NAD kinase 1

B: NAD kinase 1

C: NAD kinase 1

D: NAD kinase 1

hetero molecules

127 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	66.790, 119.180, 67.210
Angle α, β, γ (deg.)	90.00, 99.91, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	NAD kinase 1 / ATP-dependent NAD kinase Mass: 31045.279 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) (bacteria) Gene: nadK1, lmo0968 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8Y8D7, NAD+ kinase
#2: Chemical	ChemComp-CIT / CITRIC ACID Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₈O₇
#3: Chemical	ChemComp-5AK / 8-[(2-{[2-(3-bromophenyl)ethyl]amino}-2-oxoethyl)sulfanyl]adenosine Mass: 539.403 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₀H₂₃BrN₆O₅S
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.12 Å³/Da / Density % sol: 42.03 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 30 mM sodium bromide, 220 mM potassium citrate, pH 4.8-5.1, glycerol 6%, 15-16% w/v polyethylene glycol 400

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID14-1 / Wavelength: 0.9334 Å

Detector

Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 11, 2012

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9334 Å / Relative weight: 1

Reflection

Resolution: 2.29→66.207 Å / Num. all: 43420 / Num. obs: 43420 / % possible obs: 93.1 % / Redundancy: 3 % / B_iso Wilson estimate: 36.64 Å² / R_pim(I) all: 0.029 / R_rim(I) all: 0.051 / R_sym value: 0.035 / Net I/av σ(I): 15.897 / Net I/σ(I): 20.1 / Num. measured all: 128384

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_pim(I) all	R_sym value	Net I/σ(I) obs	% possible all
2.29-2.41	3.1	0.443	1.3	20948	6789	0.354	0.443	2.7	100
2.41-2.56	3.1	0.358	1.6	19997	6431	0.281	0.358	3.4	100
2.56-2.74	3	0.245	2.4	14247	4676	0.197	0.245	4.7	77.6
2.74-2.96	2.9	0.146	4	16514	5628	0.119	0.146	7.1	100
2.96-3.24	2.8	0.069	8.9	14694	5160	0.058	0.069	13.2	100
3.24-3.62	2.8	0.03	21.6	11469	4112	0.025	0.03	24.9	87.5
3.62-4.18	2.8	0.015	42	7998	2880	0.013	0.015	40.9	69.1
4.18-5.12	2.9	0.01	56.2	10317	3513	0.008	0.01	61	100
5.12-7.24	2.8	0.011	52.1	7501	2714	0.009	0.011	57.9	100
7.24-44.292	3.1	0.009	50.8	4699	1517	0.006	0.009	71.8	99.5

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
SCALA	3.3.21	data scaling
PDB_EXTRACT	3.15	data extraction
MOSFLM		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2i1w

2i1w

Resolution: 2.29→44.292 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 41.9 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.3106	2505	3.03 %
R_work	0.26	-	-
obs	0.2616	41997	89.94 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.29→44.292 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8120	0	164	198	8482

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	8488
X-RAY DIFFRACTION	f_angle_d	0.601	11493
X-RAY DIFFRACTION	f_dihedral_angle_d	10.85	3081
X-RAY DIFFRACTION	f_chiral_restr	0.024	1252
X-RAY DIFFRACTION	f_plane_restr	0.002	1461

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 (%)
2.29-2.334	0.5083	121	0.5248	4616	X-RAY DIFFRACTION	92
2.334-2.3817	0.5043	134	0.5013	4647	X-RAY DIFFRACTION	93
2.3817-2.4335	0.5396	161	0.5015	4509	X-RAY DIFFRACTION	93
2.4335-2.4901	0.5346	160	0.4597	4731	X-RAY DIFFRACTION	94
2.4901-2.5523	0.4674	149	0.4434	4586	X-RAY DIFFRACTION	95
2.5523-2.6213	0.4734	126	0.4005	4786	X-RAY DIFFRACTION	95
2.6213-2.6985	0.3508	62	0.3922	2248	X-RAY DIFFRACTION	45
2.6985-2.7856	0.4461	134	0.3538	4863	X-RAY DIFFRACTION	97
2.7856-2.8851	0.3598	149	0.3241	4774	X-RAY DIFFRACTION	97
2.8851-3.0006	0.3629	138	0.3047	4813	X-RAY DIFFRACTION	98
3.0006-3.1371	0.3192	179	0.2802	4834	X-RAY DIFFRACTION	99
3.1371-3.3025	0.3183	141	0.2519	4914	X-RAY DIFFRACTION	99
3.3025-3.5093	0.303	148	0.2203	3843	X-RAY DIFFRACTION	77
3.5093-3.7801	0.3682	110	0.2137	3439	X-RAY DIFFRACTION	70
3.7801-4.1603	0.2011	121	0.1799	3760	X-RAY DIFFRACTION	76
4.1603-4.7616	0.2026	167	0.1487	4948	X-RAY DIFFRACTION	100
4.7616-5.9968	0.2224	157	0.1788	4934	X-RAY DIFFRACTION	100
5.9968-44.3	0.2621	148	0.2194	4929	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	3.0835	0.831	-0.2838	3.9436	-1.4232	1.9163	0.1175	-0.1996	-0.3697	0.7175	-0.1873	0.016	0.2746	-0.0382	0.0569	0.7252	-0.1042	0.0859	0.2582	0.0063	0.4789	5.1266	-30.7875	-26.1525
2	2.54	2.0716	-0.7483	3.1187	-0.7576	3.3397	0.1673	-0.0096	-0.0789	0.2931	-0.0737	0.3068	0.1152	-0.3216	-0.12	0.3072	-0.0065	0.0205	0.1881	-0.0424	0.3095	9.8273	-6.901	-38.5117
3	3.4049	1.1456	0.7315	3.4991	1.2602	1.594	0.353	-0.7628	0.9143	0.4686	-0.1322	-0.3048	-0.5572	0.4908	-0.1927	0.9139	-0.4161	-0.0136	0.7645	-0.1167	0.7752	35.7582	17.5004	-24.1425
4	2.6646	0.725	-0.3634	1.4808	0.1348	2.6254	0.1437	-0.4662	-0.3387	0.5081	-0.1976	-0.7883	0.1017	0.7339	0.0152	0.3875	-0.0555	-0.196	0.4445	0.1135	0.6886	34.5009	-7.3637	-33.8965
5	2.6484	-0.9429	1.5084	3.5623	-2.6722	3.874	0.2334	0.8644	1.0414	-0.7107	-0.1172	0.1692	-0.5044	-0.3173	-0.086	0.7858	0.2425	0.0094	0.8322	0.3348	0.8516	5.8817	8.4622	-77.3264
6	4.4477	-0.3124	-0.2393	2.5498	0.6828	2.902	0.1127	0.7334	-0.5029	-0.2203	-0.1659	-0.0835	0.2225	-0.1267	0.0426	0.339	0.1143	-0.0045	0.3643	-0.0757	0.2826	15.2189	-13.3263	-64.6078
7	4.8858	-2.6935	-2.4138	5.0193	2.95	3.4605	0.1221	0.8037	-0.6843	0.1594	-0.2924	0.1351	0.6017	0.5942	0.1582	0.6525	0.3677	0.1032	1.139	-0.0923	0.9115	50.7832	-24.5131	-69.7008
8	3.1017	-0.898	-0.234	1.0475	0.0848	2.0623	0.2439	0.4386	0.2181	-0.1295	-0.1185	-0.9849	-0.068	0.449	-0.1369	0.2628	0.0716	0.1418	0.5116	0.0768	0.6024	38.0412	-3.682	-60.9742

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 1:100)
2	X-RAY DIFFRACTION	2	(chain A and resid 101:264)
3	X-RAY DIFFRACTION	3	(chain B and resid 1:100)
4	X-RAY DIFFRACTION	4	(chain B and resid 101:264)
5	X-RAY DIFFRACTION	5	(chain C and resid 1:100)
6	X-RAY DIFFRACTION	6	(chain C and resid 101:264)
7	X-RAY DIFFRACTION	7	(chain D and resid 1:100)
8	X-RAY DIFFRACTION	8	(chain D and resid 101:264)

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