PDB-5ejf: Crystal structure of NAD kinase P101A mutant from Listeria monocy...

ID or keywords:

Entry

Database: PDB / ID: 5ejf

Title

Crystal structure of NAD kinase P101A mutant from Listeria monocytogenes

Components

NAD kinase 1

Keywords

TRANSFERASE / Gram-positive NAD Kinase / allostery / citrate

Function / homology

Function and homology information

NAD+ kinase / NADP biosynthetic process / NAD+ kinase activity / NAD metabolic process / NAD binding / phosphorylation / ATP binding / metal ion binding / cytoplasm
Similarity search - Function

Biological species

Listeria monocytogenes (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.12 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: P101A 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 / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5ejf.cif.gz	412.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5ejf.ent.gz	338.9 KB	Display	PDB format
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Validation report

Summary document	5ejf_validation.pdf.gz	463.7 KB	Display	wwPDB validaton report
Full document	5ejf_full_validation.pdf.gz	490 KB	Display
Data in XML	5ejf_validation.xml.gz	45.3 KB	Display
Data in CIF	5ejf_validation.cif.gz	63.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ej/5ejf ftp://data.pdbj.org/pub/pdb/validation_reports/ej/5ejf	HTTPS FTP

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Related structure data

Related structure data	2i1wS S: Starting model for refinement
Similar structure data	5ejg-d 5dht-d 6rc1-1 2i1w-d 2i2a-1 6rbu-1 6rc0-1 6rbr-1 6rc4-1 1u0t-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)	67.042, 119.174, 67.593
Angle α, β, γ (deg.)	90.000, 100.980, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	chain A
2	1	chain B
3	1	chain C
4	1	chain D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET

Dom-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	ILE	ILE	chain A	A	A	1 - 262	1 - 262
2	HIS	HIS	chain B	B	B	1 - 267	1 - 267
3	GLU	GLU	chain C	C	C	1 - 263	1 - 263
4	GLU	GLU	chain D	D	D	1 - 263	1 - 263

#1: Protein	NAD kinase 1 / ATP-dependent NAD kinase Mass: 31019.244 Da / Num. of mol.: 4 / Fragment: NAD Kinase 1-264 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.: 508 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

NAD kinase 1 / ATP-dependent NAD kinase

Mass: 31019.244 Da / Num. of mol.: 4 / Fragment: NAD Kinase 1-264
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.: 508 / 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: 2.14 Å³/Da / Density % sol: 42.43 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.1 Details: 50 mM Sodium Bromide, 150 mM tri-sodium citrate dihydrate, 14-16% w/v polyethylene glycol 400 PH range: 5.1-5.4

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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: 2.04→66.355 Å / Num. all: 58778 / Num. obs: 58778 / % possible obs: 99.6 % / Redundancy: 6 % / R_pim(I) all: 0.048 / R_rim(I) all: 0.119 / R_sym value: 0.109 / Net I/av σ(I): 4.77 / Net I/σ(I): 11.2 / Num. measured all: 351556

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
2.12-2.23	5.4	0.633	1.2	45655	8470	0.294	0.633	2.6	98.5
2.23-2.37	6.2	0.463	1.6	50022	8129	0.2	0.463	3.9	100
2.37-2.53	6.2	0.319	2.3	47061	7638	0.137	0.319	5.4	99.9
2.53-2.74	6.2	0.202	3.6	43754	7087	0.087	0.202	8	99.9
2.74-3	6.1	0.146	5	40232	6548	0.063	0.146	10.7	99.7
3-3.35	6.1	0.095	7.1	36383	5942	0.041	0.095	15.6	99.8
3.35-3.87	6	0.072	8.6	31424	5220	0.031	0.072	20.6	99.8
3.87-4.74	5.9	0.074	7.4	26329	4438	0.032	0.074	23.8	99.6
4.74-6.7	5.6	0.065	8.1	19159	3401	0.029	0.065	23.8	98.9
6.7-34.776	6.1	0.052	7.8	11537	1905	0.023	0.052	27.6	99.4

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2I1W

2i1w

Resolution: 2.12→34.776 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 29.53 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2685	5887	5.08 %
R_work	0.2116	110074	-
obs	0.2145	58737	99.44 %

Solvent computation

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

Displacement parameters

B_iso max: 135.39 Å² / B_iso mean: 45.4889 Å² / B_iso min: 9.62 Å²

Refinement step

Cycle: final / Resolution: 2.12→34.776 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7866	0	0	508	8374
B_iso mean	-	-	-	44.28	-
Num. residues	-	-	-	-	1008

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	8048
X-RAY DIFFRACTION	f_angle_d	1.239	10890
X-RAY DIFFRACTION	f_chiral_restr	0.065	1218
X-RAY DIFFRACTION	f_plane_restr	0.008	1384
X-RAY DIFFRACTION	f_dihedral_angle_d	13.751	2853

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	4518	X-RAY DIFFRACTION	11.94	TORSIONAL
1	2	B	4518	X-RAY DIFFRACTION	11.94	TORSIONAL
1	3	C	4518	X-RAY DIFFRACTION	11.94	TORSIONAL
1	4	D	4518	X-RAY DIFFRACTION	11.94	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.1197-2.1438	0.3704	168	0.2816	3467	3635	93
2.1438-2.169	0.3352	208	0.2783	3593	3801	97
2.169-2.1954	0.3465	201	0.2828	3649	3850	100
2.1954-2.2232	0.3346	176	0.2754	3725	3901	100
2.2232-2.2524	0.3823	217	0.2704	3734	3951	100
2.2524-2.2833	0.3378	208	0.2657	3569	3777	100
2.2833-2.3159	0.3222	178	0.2443	3797	3975	100
2.3159-2.3505	0.3037	228	0.237	3573	3801	100
2.3505-2.3872	0.3178	205	0.2529	3706	3911	100
2.3872-2.4263	0.3498	178	0.2494	3710	3888	100
2.4263-2.4681	0.3503	166	0.2603	3705	3871	100
2.4681-2.513	0.3376	197	0.2429	3714	3911	100
2.513-2.5613	0.3116	178	0.2232	3661	3839	100
2.5613-2.6136	0.3052	228	0.2132	3684	3912	100
2.6136-2.6704	0.2998	185	0.2183	3685	3870	100
2.6704-2.7325	0.2734	211	0.2331	3690	3901	100
2.7325-2.8008	0.295	213	0.2204	3664	3877	100
2.8008-2.8765	0.2865	198	0.2295	3641	3839	100
2.8765-2.9611	0.2609	216	0.2223	3670	3886	100
2.9611-3.0566	0.3172	195	0.2246	3761	3956	100
3.0566-3.1658	0.3283	192	0.2223	3625	3817	100
3.1658-3.2925	0.2665	195	0.2143	3649	3844	100
3.2925-3.4422	0.2714	175	0.2098	3726	3901	100
3.4422-3.6235	0.2255	221	0.1862	3613	3834	100
3.6235-3.8502	0.2216	192	0.1815	3717	3909	100
3.8502-4.1471	0.2385	187	0.1767	3676	3863	100
4.1471-4.5636	0.2174	190	0.1743	3704	3894	100
4.5636-5.222	0.1937	217	0.1699	3638	3855	99
5.222-6.572	0.2569	205	0.2032	3619	3824	99
6.572-34.7804	0.2172	159	0.2131	3709	3868	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	0.0194	0.0095	0.0185	0.0036	-0.0065	0.0195	0.1241	0.0815	-0.0953	0.0279	0.04	-0.0581	0.0308	0.0001	-0.0071	0.5148	-0.1226	0.1201	0.0812	0.0259	0.368	2.3076	-40.4126	-28.8538
2	0.0612	0.006	0.0355	-0	-0.0109	0.0138	0.2028	0.0187	-0.0192	0.0583	-0.0308	0.0884	0.0692	-0.045	0.0387	0.2823	-0.0604	0.0723	0.1276	0.0023	0.3044	1.1079	-28.8503	-26.1913
3	0.0062	0.0021	-0.0057	0.0054	-0.0114	-0.0025	0.088	0.0192	-0.0278	0.067	0.0647	0.0463	0.1122	-0.0145	0.0001	0.3063	0.0132	0.0091	0.2054	-0.0004	0.2993	13.1251	-32.3243	-31.3264
4	0.2843	0.1713	0.0086	0.1196	0.0067	0.1386	0.1097	0.0159	-0.0065	0.0069	-0.0759	0.1263	0.0191	-0.0409	0.0139	0.1511	0.0169	0.0106	0.1141	-0.0122	0.1498	11.6506	-10.6748	-37.5773
5	0.0333	0.0006	0.014	0.0056	-0.0235	0.0249	0.1112	0.0252	0.0937	0.053	0.0599	0.145	-0.0024	-0.0525	0.0259	0.0748	0.0278	-0.0449	0.1223	0.0085	0.2767	1.3747	-8.5425	-41.7274
6	0.0572	0.0292	0.0661	0.0068	0.0204	0.0856	0.2945	0.1485	-0.1124	0.0512	-0.0019	-0.1003	0.0604	0.2066	0.0757	0.1717	-0.2469	0.0932	-0.2149	0.0947	0.2034	18.6246	-24.9024	-29.4329
7	0.0039	0.0037	0.0002	0.0009	-0.0037	0.0009	-0.0332	0.0267	0.143	-0.0143	-0.0432	-0.0369	-0.0381	0.012	0.0001	0.5196	-0.165	-0.0193	0.4061	-0.1566	0.5227	40.1291	20.0148	-24.4487
8	0.0047	0.0002	-0.0132	0.0127	0.0244	0.0602	-0.1248	-0.1847	0.1601	-0.0143	0.0877	0.0151	0.0105	0.0859	0.0004	0.3604	-0.2094	-0.014	0.3256	-0.1785	0.2641	39.477	9.1222	-20.7648
9	0.0028	-0.0005	0.0015	0.0037	0.0025	0.0038	0.0775	-0.0432	0.142	0.0309	0.0765	0.0235	-0.0167	0.0127	0	0.3921	-0.0768	-0.0281	0.2037	-0.0343	0.2605	30.9522	12.1731	-29.5687
10	0.1102	0.0351	0.0013	0.0313	0.0057	0.0988	0.1165	-0.1473	0.065	0.0861	0.016	-0.0247	0.1148	0.0247	0.0762	0.1522	-0.015	-0.0522	0.1342	-0.0248	0.1728	34.0136	4.0843	-22.7441
11	0.0206	0.0327	0.0334	0.0136	0.0132	0.0317	0.067	0.0047	0.0379	0.0744	-0.0089	-0.0886	0.0143	0.0544	0.0016	0.1254	0.0106	-0.0292	0.1326	0.0008	0.1397	34.4692	-13.8318	-37.9763
12	0.0574	0.0859	-0.0073	0.0884	0.0217	0.0246	0.2747	-0.0107	-0.0636	0.1549	-0.1593	-0.123	0.0254	0.0907	0.1784	0.1635	0.0116	-0.0594	0.2013	-0.0023	0.1167	39.7442	-11.7306	-29.2041
13	-0.0094	0.0092	0.0144	-0.0062	0.0042	0.0035	0.0482	-0.027	0.0879	-0.0566	-0.0811	0.0846	0.0493	0.0068	-0	0.1513	0.0048	0.0376	0.1271	-0.0252	0.2797	21.3012	10.0827	-35.972
14	0.0256	-0.0114	0.003	0.0237	-0.0093	0.0087	0.0846	0.1156	0.2096	0.0593	0.0417	0.0748	0.0069	-0.0357	0.0002	0.3346	0.164	-0.0116	0.3876	0.0337	0.3856	9.6232	6.9881	-79.5459
15	0.1309	-0.0816	-0.0188	0.1418	0.0155	0.1796	0.1115	0.1598	-0.1515	0.0092	-0.1433	0.0747	-0.0456	-0.063	0.0485	0.1528	0.0186	-0.016	0.2054	-0.0861	0.1534	18.8501	-18.3459	-64.0649
16	0.0434	-0.0042	0.0022	0.0222	-0.0442	-0.01	0.1428	0.1945	-0.0372	-0.0874	-0.2487	-0.0334	-0.1	-0.1099	-0.0006	0.241	0.0641	-0.0189	0.3225	-0.0428	0.2153	16.4014	-6.879	-69.1111
17	0.0092	-0.0002	0.0013	-0.0011	0.0013	0.0066	-0.1027	0.1009	-0.0794	0.0399	-0.0185	-0.0227	0.0242	0.0285	0.0002	0.4965	0.1794	0.0094	0.486	-0.144	0.5753	59.8596	-31.2139	-68.8887
18	0.0464	-0.0229	0.0262	0.0161	-0.0118	0.018	0.0283	0.0002	-0.0113	0.057	0.1081	-0.0345	0.0211	0.1092	0.0199	-0.0135	0.2491	0.1175	0.4645	-0.2646	0.484	55.6994	-20.9833	-72.2119
19	0.0017	0.0007	0.0067	0.0014	-0.0005	0.0047	0.0858	-0.0185	-0.0596	0.0427	0.0738	0.0442	-0.0392	-0.0709	-0.0008	0.4862	0.0244	0.0975	0.4555	-0.1917	0.4613	48.2305	-32.4518	-70.6499
20	-0.001	-0.0027	-0.0145	-0.0042	0.0292	0.0022	0.185	0.1154	0.1131	-0.0884	-0.0339	-0.0622	0.0455	0.0111	0	0.222	0.0107	0.0587	0.3447	-0.0063	0.2127	48.4334	-6.4558	-67.8338
21	0.0458	-0.0396	0.008	0.0239	-0.0202	0.0363	0.0271	0.0629	0.0474	-0.0395	-0.0298	-0.0553	0.0013	0.006	0	0.1764	0.007	0.0322	0.2026	0.0245	0.134	37.3077	-1.1689	-57.47
22	0.0383	-0.0177	0.0181	0.0184	0.0112	0.0913	-0.0029	0.2882	-0.0215	0.0595	-0.03	-0.1063	-0.0426	0.1517	-0.0096	0.172	-0.0161	0.018	0.3489	-0.027	0.2276	48.1176	-6.4273	-63.3451
23	0.0169	-0.0036	-0.0018	-0.0011	-0.0021	-0.0013	-0.0199	0.0179	-0.0409	-0.1077	-0.0023	-0.0607	0.0699	0.0025	0.0008	0.2865	0.047	-0.0451	0.2744	0.0021	0.2663	33.1844	-26.6955	-61.5526

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 61 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 62 through 79 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 80 through 216 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 217 through 238 )	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 239 through 262 )	A
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 1 through 22 )	B
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 23 through 61 )	B
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 62 through 79 )	B
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 80 through 120 )	B
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 121 through 198 )	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 199 through 247 )	B
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 248 through 267 )	B
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 1 through 100 )	C
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 101 through 216 )	C
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 217 through 263 )	C
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 1 through 26 )	D
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 27 through 68 )	D
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 69 through 91 )	D
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 92 through 122 )	D
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 123 through 216 )	D
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 217 through 252 )	D
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 253 through 263 )	D

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