PDB-5ejg: Crystal structure of NAD kinase P252D mutant from Listeria monocy...

ID or keywords:

Entry

Database: PDB / ID: 5ejg

Title

Crystal structure of NAD kinase P252D mutant from Listeria monocytogenes

Components

NAD kinase 1

Keywords

TRANSFERASE / Gram-positive NAD Kinase / allostery / citrate

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 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.877 Å

Authors

Poncet-Montange, G. / Assairi, L. / Gelin, M. / Pochet, S. / Labesse, G.

Funding support

France, 1items

Citation

Journal: to be published
Title: Crystal structure of NAD kinase 1 from Listeria monocytogenes: P252D mutant
Authors: Poncet-Montange, G. / Assairi, L. / Gelin, M. / Pochet, S. / Labesse, G.

History

Deposition	Nov 1, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Nov 9, 2016	Provider: repository / Type: Initial release
Revision 1.1	Sep 6, 2017	Group: Author supporting evidence / Data collection / Category: diffrn_radiation_wavelength / pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	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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Download

PDBx/mmCIF format	5ejg.cif.gz	388.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5ejg.ent.gz	319.2 KB	Display	PDB format
PDBx/mmJSON format	5ejg.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5ejg_validation.pdf.gz	462.2 KB	Display	wwPDB validaton report
Full document	5ejg_full_validation.pdf.gz	495.3 KB	Display
Data in XML	5ejg_validation.xml.gz	40.4 KB	Display
Data in CIF	5ejg_validation.cif.gz	55 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ej/5ejg ftp://data.pdbj.org/pub/pdb/validation_reports/ej/5ejg	HTTPS FTP

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Related structure data

Related structure data	2i1wS S: Starting model for refinement
Similar structure data	5ejf-d 6rc1-1 2i1w-d 6rc4-1 6rbr-1 5dht-d 3v8p-1 5ejh-1 2i2a-1 6rg8-1 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

124 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)	67.217, 119.655, 68.624
Angle α, β, γ (deg.)	90.000, 100.920, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	NAD kinase 1 / ATP-dependent NAD kinase Mass: 31063.252 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes (bacteria) / Gene: nadK1, lmo0968 / Plasmid: pLA15.3.3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8Y8D7, NAD+ kinase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.18 Å³/Da / Density % sol: 43.6 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.1 Details: 50 mM Sodium Bromide, 150 mM tri-sodium citrate dihydrate, pH 5.1-5.4, 14-16% w/v polyethylene glycol 400

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID14-2 / Wavelength: 0.933 Å

Detector

Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 16, 2006

Radiation

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

Radiation wavelength

Wavelength: 0.933 Å / Relative weight: 1

Reflection

Resolution: 2.87→67.262 Å / Num. all: 23639 / Num. obs: 23639 / % possible obs: 97.9 % / Redundancy: 3.9 % / B_iso Wilson estimate: 45.89 Å² / R_pim(I) all: 0.097 / R_rim(I) all: 0.201 / R_sym value: 0.175 / Net I/av σ(I): 3.602 / Net I/σ(I): 6.5 / Num. measured all: 92301

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
2.87-3.03	3.9	0.632	1.2	13798	3497	0.353	0.632	2	99.7
3.03-3.21	4	0.437	1.7	13103	3316	0.244	0.437	2.8	99.4
3.21-3.43	3.9	0.298	2.5	12286	3112	0.165	0.298	3.9	99.4
3.43-3.71	3.7	0.225	3.1	10009	2671	0.129	0.225	5.3	92
3.71-4.06	3.9	0.173	4.1	10165	2629	0.096	0.173	6.7	98.5
4.06-4.54	3.9	0.119	5.5	9512	2409	0.065	0.119	9.9	98.7
4.54-5.24	3.9	0.105	6	8301	2110	0.058	0.105	11	98.4
5.24-6.42	4	0.106	6	6993	1762	0.057	0.106	10.5	98.1
6.42-9.08	3.9	0.087	7	5389	1386	0.048	0.087	12	97.6
9.08-34.951	3.7	0.072	4.2	2745	747	0.04	0.072	13.5	94.5

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Processing

Software

Name	Version	Classification
PHENIX		refinement
SCALA	3.3.21	data scaling
PDB_EXTRACT	3.15	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2I1W

2i1w

Resolution: 2.877→18.637 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 0.04 / Phase error: 36.91 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.3244	1487	3.21 %
R_work	0.217	44861	-
obs	0.2205	23531	97.58 %

Solvent computation

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

Displacement parameters

B_iso max: 205.01 Å² / B_iso mean: 63.8958 Å² / B_iso min: 0.15 Å²

Refinement step

Cycle: final / Resolution: 2.877→18.637 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7552	0	0	112	7664
B_iso mean	-	-	-	31.17	-
Num. residues	-	-	-	-	977

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	7735
X-RAY DIFFRACTION	f_angle_d	1.31	10473
X-RAY DIFFRACTION	f_chiral_restr	0.057	1177
X-RAY DIFFRACTION	f_plane_restr	0.007	1336
X-RAY DIFFRACTION	f_dihedral_angle_d	16.215	2701

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.8765-2.969	0.411	124	0.323	3959	4083	95
2.969-3.0747	0.4092	145	0.295	4207	4352	100
3.0747-3.1972	0.4013	155	0.2665	4129	4284	100
3.1972-3.3419	0.3576	113	0.2327	4171	4284	99
3.3419-3.517	0.3303	172	0.2215	4122	4294	99
3.517-3.7357	0.3216	125	0.2067	3739	3864	89
3.7357-4.0215	0.3325	126	0.2088	4138	4264	99
4.0215-4.4213	0.3194	145	0.187	4082	4227	99
4.4213-5.0499	0.2567	132	0.1749	4138	4270	99
5.0499-6.3208	0.3103	134	0.2063	4107	4241	98
6.3208-18.6373	0.2911	116	0.2161	4069	4185	97

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	-0.0023	0.0013	-0.0025	0.0024	-0.0018	0.0021	0.0018	0.0278	-0.0289	-0.0579	0.0431	-0.0222	0.0052	-0.017	-0	0.1722	-0.0211	0.0701	0.1715	0.0056	0.1948	2.7421	-40.7138	-29.0418
2	0.0026	-0.0129	0.0029	0.0004	-0.0114	-0.0096	0.0898	-0.1003	0.0176	0.0631	-0.0049	0.0694	0.0361	-0.0692	-0	-0.1986	0.2949	0.4474	-0.1897	-0.2712	-0.0186	5.3297	-30.0716	-27.9881
3	0.0185	0.0421	0.0322	0.0052	-0.0239	-0.0396	0.3331	0.1189	-0.2575	-0.0748	-0.0281	0.0921	0.0325	-0.0501	0	-0.285	-0.0796	0.4215	0.1442	0.169	-0.3784	10.1124	-14.5827	-35.8477
4	-0.0062	-0.0038	-0.0031	0.0078	0.0061	-0.0027	0.1834	-0.0767	-0.0317	0.1193	-0.0664	-0.0623	-0.004	-0.0976	-0	-0.0646	-0.0382	0.2885	0.0056	0.0766	-0.2465	18.0682	-5.8004	-43.1244
5	0.0079	0.0057	-0.0113	0.0048	-0.0119	-0.0041	0.0951	0.0356	-0.0028	0.0632	-0.06	0.0925	-0.0204	-0.0103	0	0.071	0.022	0.0108	0.0626	-0.0001	0.0731	4.1984	-5.8262	-41.3186
6	0.0049	0.0109	-0.0136	0.0083	-0.0107	-0.0003	-0.0518	-0.1147	0.0424	0.0078	-0.156	0.0127	0.0446	0.0183	0	0.2168	-0.0511	0.0637	0.1452	-0.0175	0.3424	16.3617	-20.7223	-31.0743
7	-0.0006	0.0042	-0.0019	-0.0002	0.0029	0.0013	0.0073	-0.0498	0.0365	0.0204	-0.0005	-0.0173	0.0144	0.0056	0	0.5532	-0.1213	-0.0779	0.4732	-0.0254	0.5927	40.3135	20.3853	-25.9108
8	0.0056	0.0025	-0.0052	0.0045	0.0029	-0.0028	0.0364	-0.0159	-0.0345	-0.0055	0.0298	-0.0126	-0.0243	-0.0386	0	0.3945	-0.067	-0.198	0.2613	-0.1176	0.4816	38.9881	13.7882	-21.2246
9	-0.0006	-0.0039	0.0003	0.0103	0.0055	0.0046	0.0764	0.1306	-0.0103	0.0446	0.0641	0.0127	-0.0153	-0.0526	-0	0.4775	0.0144	-0.2108	0.041	0.0132	0.2711	33.6187	9.6857	-25.4989
10	0.0005	-0.0003	0.0032	0.0007	-0.0019	0.0093	0.0317	0.0097	0.05	-0.0194	-0	-0.0058	-0.0007	-0.018	0	0.3068	0.0189	-0.0387	0.0084	-0.0675	0.1376	27.1952	15.3546	-21.5397
11	0.0106	-0.0043	-0.0008	-0.0022	0.0012	0.0149	-0.0414	0.0843	-0.0066	0.0287	0.1433	-0.0027	0.0266	-0.009	-0	0.1239	-0.0565	-0.0605	0.1044	-0.0061	0.0771	38.7213	-12.9328	-35.2609
12	-0.001	-0.0165	0.0181	0.0054	0.0055	-0.0035	0.0931	0.021	-0.0203	0.0422	-0.0512	-0.0036	0.0353	0.1291	-0	-0.1028	-0.0015	-0.226	0.0917	-0.0124	-0.0474	31.3895	-15.1362	-36.7914
13	0.004	-0.0011	0.0058	-0.0015	-0.0035	-0.0013	-0.007	0.0296	-0.0288	-0.0009	0.0145	-0.0246	-0.0095	0.0166	0	0.0426	-0.0514	-0.3007	0.1163	0.1642	0.1926	48.5421	-11.9241	-35.0074
14	-0.0074	-0.0073	-0.0066	-0.0026	0.0053	-0.001	0.072	0.002	0.0113	0.0223	0.0334	-0.0217	-0.0145	0.0206	0	0.2043	-0.1137	-0.2696	0.0615	-0.0469	0.0472	30.0309	-0.3118	-24.2313
15	0.0007	0.0031	0.001	0.0022	0.0002	0.0022	-0.047	-0.0254	0.0412	-0.0045	0.0148	0.0072	-0.0081	0.0241	-0	0.3575	-0.0411	-0.0279	0.2561	-0.0547	0.4892	21.2794	8.6625	-39.9454
16	0.0007	-0.0053	0.0026	-0.0018	0.0011	0.002	-0.0417	0.0179	0.0286	0.0159	0.038	0.0421	0.0217	-0.0216	-0	0.5977	0.2618	-0.1141	0.6014	-0.001	0.6167	4.867	10.076	-81.8917
17	0.0006	-0.0007	-0.0016	-0.0001	0.001	0.002	-0.0123	0.0035	-0.027	-0.0084	-0.0226	0.0126	-0.0043	0.0018	0	0.6574	0.1688	-0.1662	0.6338	0.0276	0.5455	10.133	-0.1141	-76.0368
18	0.0051	-0.0004	-0.0048	0.0052	0.0021	0.0035	0.0134	-0.0079	0.0479	0.0205	0.0433	0.0018	0.0344	0.0003	-0	0.6562	0.2523	-0.1478	0.3358	0.0495	0.4699	16.5403	8.8113	-76.9898
19	-0.0358	0.0007	-0.0035	-0.0178	0.0056	-0.0004	0.1046	0.0961	-0.1181	0.0312	-0.1602	0.0473	-0.0875	-0.0316	-0	0.1018	0.2269	0.1413	-0.6618	-1.0166	-0.8442	16.1538	-18.2326	-65.4029
20	-0.0024	-0.0061	-0.0034	-0.0277	-0.0384	-0.0225	0.1771	-0.0346	-0.0764	-0.2079	-0.1116	-0.0866	-0.0829	-0.0917	-0	-0.2369	0.0706	-0.2641	-0.2076	-0.5811	-0.5321	24.246	-16.8247	-62.3142
21	0.001	0.0011	0.0005	-0.0002	0.0045	-0.0001	0.0489	-0.0005	-0.0192	0.013	0.0354	-0.0064	-0.0323	-0.0225	0	-0.0002	0.1124	-0.1084	0.0784	-0.2525	0.1253	10.3426	-24.4625	-63.8789
22	0.0028	-0.0002	0.0153	-0.0059	-0.0039	0.0011	-0.0589	-0.0067	-0.0602	-0.0473	-0.036	0.0178	-0.0135	0.007	-0	0.0346	0.3385	-0.2461	0.2052	-0.2122	0.1607	10.5705	-18.4992	-70.7483
23	-0.003	0.0027	0.0055	0.0075	-0.0007	0.0001	-0.0159	-0.0809	0.0091	0.0194	-0.0197	-0.0033	-0.0001	-0.0212	0	0.4545	0.0581	0.0335	0.0831	0.0067	0.1369	23.58	5.8699	-69.492
24	0.007	-0.0014	-0.0017	-0.0048	0.0053	-0.0013	-0.02	-0.0225	0.0081	-0.032	0.0016	-0.0363	-0.0067	0.0142	-0	0.0357	0.1363	0.1659	0.4808	-0.0818	0.1863	60.3386	-29.6612	-72.7513
25	-0.0038	-0.002	-0.0023	-0.01	0.0007	-0.0051	0.1616	-0.0287	-0.0342	0.0694	0.0641	0.0057	0.0837	-0.0022	-0	-0.1336	0.3651	0.1908	0.3482	-0.2221	0.1856	50.9095	-24.8691	-70.3003
26	0.0233	0.0073	0.0211	-0.0106	0.0257	-0.0194	0.4756	-0.0109	-0.0573	-0.1495	0.0919	-0.075	0.0194	-0.0032	0	-0.5834	0.1995	0.1539	0.0653	0.0228	-0.0323	39.2677	-3.4782	-60.3044
27	0.0041	0.0014	-0.0012	-0.001	0.0014	-0.002	0.0645	-0.018	0.0886	-0.0324	0.0346	-0.0484	0.0192	0.0273	-0	0.2146	0.0533	0.1272	0.2167	0.0289	0.0404	40.8159	3.7439	-61.8865
28	0.0049	-0.0078	-0.0109	0.0022	0.0033	0.0015	-0.0242	0.0585	-0.0549	-0.0113	-0.0619	-0.0357	0.0179	-0.0373	-0	0.126	0.1707	0.1483	0.1378	0.0621	0.2724	49.7653	-1.099	-59.4333
29	-0.0052	0.0043	-0.0018	-0.0028	0.0057	0.0029	0.0739	0.0127	-0.1267	-0.0371	0.0141	0.03	0.046	-0.0023	0	0.2445	0.1379	0.1133	0.4669	-0.1506	0.3026	37.7323	-23.4557	-68.6363

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 26 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 27 through 79 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 80 through 167 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 168 through 198 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 199 through 232 )	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 233 through 262 )	A
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 1 through 21 )	B
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 22 through 54 )	B
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 55 through 79 )	B
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 80 through 101 )	B
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 102 through 167 )	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 168 through 211 )	B
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 212 through 233 )	B
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 234 through 252 )	B
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 253 through 266 )	B
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 13 through 44 )	C
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 45 through 66 )	C
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 67 through 100 )	C
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 101 through 166 )	C
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 167 through 206 )	C
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 207 through 221 )	C
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 222 through 242 )	C
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 243 through 262 )	C
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 2 through 37 )	D
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 38 through 90 )	D
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 91 through 198 )	D
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 199 through 217 )	D
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 218 through 238 )	D
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 239 through 263 )	D

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-Basic information

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-Download

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+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

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Open data

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Basic information

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Structure visualization

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Downloads & links

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Download

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Validation report

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Related structure data

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Links

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Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi