PDB-2i1w: Crystal structure of NAD kinase 1 from Listeria monocytogenes

ID or keywords:

Entry

Database: PDB / ID: 2i1w

Title

Crystal structure of NAD kinase 1 from Listeria monocytogenes

Components

Probable inorganic polyphosphate/ATP-NAD kinase 1

Keywords

TRANSFERASE / Gram-positive NAD kinase / (EC 2.7.1.23)

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: 2.34 Å

Authors

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

Citation

Journal: J.Biol.Chem. / Year: 2007
Title: NAD kinases use substrate-assisted catalysis for specific recognition of NAD.
Authors: Poncet-Montange, G. / Assairi, L. / Arold, S. / Pochet, S. / Labesse, G.

History

Deposition	Aug 15, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 7, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Derived calculations ...Advisory / Derived calculations / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2	Feb 14, 2018	Group: Experimental preparation / Category: exptl_crystal_grow Item: _exptl_crystal_grow.method / _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.3	Jun 24, 2020	Group: Advisory / Database references / Derived calculations Category: database_PDB_caveat / pdbx_distant_solvent_atoms ...database_PDB_caveat / pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_ref_seq_dif Item: _struct_ref_seq_dif.details
Revision 1.4	Aug 30, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2i1w.cif.gz	220.6 KB	Display	PDBx/mmCIF format
PDB format	pdb2i1w.ent.gz	177.4 KB	Display	PDB format
PDBx/mmJSON format	2i1w.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	2i1w_validation.pdf.gz	471.7 KB	Display	wwPDB validaton report
Full document	2i1w_full_validation.pdf.gz	509.4 KB	Display
Data in XML	2i1w_validation.xml.gz	43.6 KB	Display
Data in CIF	2i1w_validation.cif.gz	60.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/i1/2i1w ftp://data.pdbj.org/pub/pdb/validation_reports/i1/2i1w	HTTPS FTP

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Related structure data

Related structure data	2i29C 2i2aC 2i2bC 2i2cC 2i2dC 2i2fC 2q5fC 4dy6C 1u0rS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5ejf-d 5ejg-d 6rc4-1 6rby-1 6rc0-1 5ejh-1 6rbr-1 3v8q-1 6rbu-1 6rbs-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: Probable inorganic polyphosphate/ATP-NAD kinase 1

B: Probable inorganic polyphosphate/ATP-NAD kinase 1

C: Probable inorganic polyphosphate/ATP-NAD kinase 1

D: Probable inorganic polyphosphate/ATP-NAD kinase 1

hetero molecules

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	66.612, 119.017, 67.937
Angle α, β, γ (deg.)	90.00, 102.08, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Probable inorganic polyphosphate/ATP-NAD kinase 1 / PolyP / /ATP NAD kinase 1 Mass: 31045.279 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: EGD-e / Gene: ppnK1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8Y8D7, NAD+ kinase
#2: Chemical	ChemComp-IOD / IODIDE ION Mass: 126.904 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: I
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 359 / 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: 2.17 Å³/Da / Density % sol: 43.27 %
Crystal grow	Method: vapor diffusion, hanging drop / pH: 5.4 Details: 0.3 M potassium chloride, 50 mM tri-sodium citrate, 15-20% w/v polyethylene glycol 400, 10 mM KI, pH 5.4, VAPOR DIFFUSION, HANGING DROP, pH 5.40

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97976
Detector	Date: May 5, 2004
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97976 Å / Relative weight: 1
Reflection	Resolution: 2.34→34.37 Å / Num. obs: 42609 / % possible obs: 97.5 % / Observed criterion σ(I): 1 / Redundancy: 3.5 % / R_merge(I) obs: 0.066 / Net I/σ(I): 13.9

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Processing

Software

Name	Version	Classification
SCALA		data scaling
REFMAC	5.2.0005	refinement
PDB_EXTRACT	2	data extraction
MOSFLM		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1U0R

1u0r

Resolution: 2.34→34.37 Å / Cor.coef. F_o:F_c: 0.947 / Cor.coef. F_o:F_c free: 0.915 / SU B: 20.52 / SU ML: 0.223 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.509 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25696	1330	3.1 %	RANDOM
R_work	0.19408	-	-	-
obs	0.19607	41254	97.49 %	-
all	-	43681	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 37.698 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.21 Å²	0 Å²	0.52 Å²
2-	-	1.71 Å²	0 Å²
3-	-	-	1.72 Å²

Refinement step

Cycle: LAST / Resolution: 2.34→34.37 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8157	0	18	359	8534

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.021	8359
X-RAY DIFFRACTION	r_bond_other_d	0.006	0.02	7507
X-RAY DIFFRACTION	r_angle_refined_deg	1.374	1.936	11304
X-RAY DIFFRACTION	r_angle_other_deg	0.934	3	17380
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	9.778	5	1025
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.277	23.325	382
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.126	15	1382
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.786	15	48
X-RAY DIFFRACTION	r_chiral_restr	0.132	0.2	1239
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	9296
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	1796
X-RAY DIFFRACTION	r_nbd_refined	0.197	0.2	1344
X-RAY DIFFRACTION	r_nbd_other	0.205	0.2	7355
X-RAY DIFFRACTION	r_nbtor_refined	0.178	0.2	3799
X-RAY DIFFRACTION	r_nbtor_other	0.086	0.2	4493
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.307	0.2	345
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.113	0.2	2
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.34	0.2	12
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.264	0.2	32
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.615	0.2	16
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.636	1.5	5172
X-RAY DIFFRACTION	r_mcbond_other	0.116	1.5	2110
X-RAY DIFFRACTION	r_mcangle_it	0.912	2	8250
X-RAY DIFFRACTION	r_scbond_it	1.56	3	3497
X-RAY DIFFRACTION	r_scangle_it	2.197	4.5	3054
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.34→2.401 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.352	107	-
R_work	0.268	3068	-
obs	-	-	99.03 %

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	3.3693	0.9325	-0.1868	10.2211	-2.3976	1.7634	0.1518	-0.0226	-0.0325	-0.0962	-0.0673	0.4905	0.3414	-0.0759	-0.0845	0.3523	-0.1105	-0.0143	-0.4487	-0.0121	-0.0809	4.321	-33.24	-27.759
2	3.5294	1.5519	-0.588	6.0912	-1.2401	1.2241	0.1003	-0.5123	-0.4904	0.4916	-0.3851	-0.6623	0.295	0.3157	0.2849	0.5217	-0.0734	-0.0404	-0.3572	0.0588	-0.0347	14.976	-34.831	-22.269
3	7.8036	2.9507	1.6803	10.2472	2.749	11.6338	0.4254	0.3294	-1.2142	0.0486	-0.0289	-0.4724	0.9652	0.6256	-0.3965	0.1808	0.0695	-0.1139	-0.3725	-0.0681	0.166	25.833	-27.229	-36.617
4	1.7584	0.986	-0.9395	3.1075	-0.9687	3.0228	0.0624	0.3547	0.0349	0.0119	0.0438	0.5282	0.0057	-0.4378	-0.1063	0.0333	0.0189	-0.0062	-0.389	-0.0101	-0.196	9.833	-7.153	-40.562
5	4.3949	0.5828	0.405	9.7301	2.0478	4.3247	0.0666	-0.5136	0.7322	0.2969	0.043	-0.2586	-0.8053	0.392	-0.1096	0.4323	-0.2082	-0.0126	-0.2391	-0.1303	-0.0474	37.766	13.543	-21.864
6	5.9991	5.0491	-3.5169	13.4649	-0.5903	10.5966	0.3327	-0.4939	1.43	0.7887	-0.1624	0.616	-1.1523	-0.3933	-0.1703	0.3791	-0.0115	0.0409	-0.2058	-0.2021	0.1744	25.905	15.489	-21.526
7	4.6179	2.312	-3.6498	12.065	-9.4559	10.9185	0.3697	-0.286	0.3764	0.4832	-0.1248	0.2605	-0.9628	-0.1209	-0.2449	0.1296	0.0159	0.0123	-0.4839	-0.0117	-0.1897	21.47	8.418	-39.298
8	2.8532	0.5019	-0.2551	2.8742	0.5639	3.7055	0.1191	-0.0332	-0.3987	0.1589	-0.0984	-0.4446	0.2596	0.7218	-0.0207	0.0874	0.035	-0.0902	-0.3127	0.0464	-0.1925	37.458	-12.959	-34.102
9	5.7014	-2.8259	3.1832	6.7814	-1.4293	5.2345	0.1005	-0.3537	0.5099	-0.6865	-0.1531	0.1373	-0.6182	-0.8729	0.0526	0.4228	0.1014	-0.0366	-0.0415	-0.0446	-0.0369	8.666	6.229	-80.052
10	1.4772	-3.0407	-1.0066	8.4838	-3.6594	15.4492	-0.1844	0.7548	1.1417	-0.3157	-0.159	0.3014	-0.804	0.2147	0.3434	0.3072	-0.0142	-0.0224	0.0784	0.0877	0.2458	18.923	12.206	-79.401
11	6.5634	-5.6511	-4.4316	5.6095	0.0275	22.2803	0.3866	0.5167	0.6033	0.2478	-0.1321	-0.2451	-1.2015	-0.492	-0.2545	0.1101	0.0492	0.0194	-0.2734	0.1218	-0.1804	25.926	6.931	-63.093
12	2.5778	-0.4582	0.0611	2.0726	-0.1243	2.8883	0.0356	0.405	-0.4504	-0.1354	-0.1155	0.2136	0.1477	-0.4346	0.0799	0.0296	-0.0076	-0.0349	-0.1376	-0.115	-0.2169	17.45	-17.843	-66.407
13	7.3726	-1.161	-1.5749	6.2709	0.6004	2.4632	-0.0915	0.2541	-0.621	0.0636	-0.0745	-0.547	0.4172	0.2659	0.166	0.1896	0.1174	-0.0026	-0.073	0.0303	-0.0064	56.18	-24.891	-71.305
14	4.2329	-5.1481	1.9388	11.2405	1.7192	4.2265	0.1387	1.0858	-1.1127	-0.3728	-0.2279	-0.3628	0.5718	-0.2579	0.0892	0.1801	0.0608	0.0478	0.1665	-0.1307	0.2566	46.896	-30.644	-75.969
15	1.7224	5.2507	0.1086	16.2093	-1.6873	20.0948	-0.1669	-0.0653	-0.9966	-0.0171	-0.0631	-0.2765	1.4225	0.5351	0.23	-0.1003	0.0786	0.0173	-0.1896	-0.0321	0.1043	33.654	-26.597	-62.571
16	2.1096	-1.0428	-0.7969	2.6026	0.5617	2.1814	0.0967	0.0642	0.2442	-0.0587	-0.0303	-0.4522	-0.2963	0.2848	-0.0664	0.0413	-0.0412	-0.0045	-0.2453	0.0593	-0.1823	41.881	-1.792	-60.065
17	0.9173	0.1702	-0.1132	0.4734	-0.0786	0.548	0.0714	0.1925	-0.0158	0.0675	-0.0606	-0.0167	0.0343	0.031	-0.0108	0.0788	0.0017	-0.0363	-0.4022	-0.0018	-0.2382	25.585	-13.653	-49.515
18	0.3649	0.0283	-0.2141	0.3219	-0.0857	0.5512	0.0301	0.0651	-0.0303	0.031	-0.045	-0.027	-0.0304	0.0305	0.0149	0.1158	-0.0068	-0.0403	-0.2624	-0.0031	-0.1611	26.36	-9.93	-48.759

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 76
2	X-RAY DIFFRACTION	2	A	77 - 97
3	X-RAY DIFFRACTION	2	A	245 - 251
4	X-RAY DIFFRACTION	3	A	252 - 263
5	X-RAY DIFFRACTION	4	A	98 - 244
6	X-RAY DIFFRACTION	5	B	1 - 76
7	X-RAY DIFFRACTION	6	B	77 - 97
8	X-RAY DIFFRACTION	6	B	245 - 251
9	X-RAY DIFFRACTION	7	B	252 - 266
10	X-RAY DIFFRACTION	8	B	98 - 244
11	X-RAY DIFFRACTION	9	C	1 - 76
12	X-RAY DIFFRACTION	10	C	77 - 97
13	X-RAY DIFFRACTION	10	C	245 - 251
14	X-RAY DIFFRACTION	11	C	252 - 263
15	X-RAY DIFFRACTION	12	C	98 - 244
16	X-RAY DIFFRACTION	13	D	1 - 76
17	X-RAY DIFFRACTION	14	D	77 - 97
18	X-RAY DIFFRACTION	14	D	245 - 251
19	X-RAY DIFFRACTION	15	D	252 - 263
20	X-RAY DIFFRACTION	16	D	98 - 244
21	X-RAY DIFFRACTION	17	A	501 - 534
22	X-RAY DIFFRACTION	18	A	535 - 633
23	X-RAY DIFFRACTION	18	C	524 - 598
24	X-RAY DIFFRACTION	18	B	536 - 626
25	X-RAY DIFFRACTION	18	D	521 - 611

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