PDB-4lkv: Determinants of lipid substrate and membrane binding for the tetr...

ID or keywords:

Entry

Database: PDB / ID: 4lkv

Title

Determinants of lipid substrate and membrane binding for the tetraacyldisaccharide-1-phosphate 4 -kinase LpxK

Components

Tetraacyldisaccharide 4'-kinase

Keywords

TRANSFERASE / P-loop containing nucleotide triphosphate hydrolase / Kinase / Membrane Protein

Function / homology

Function and homology information

tetraacyldisaccharide 4'-kinase / lipid-A 4'-kinase activity / lipopolysaccharide core region biosynthetic process / lipid A biosynthetic process / ATP binding / plasma membrane
Similarity search - Function

Biological species

Aquifex aeolicus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

molecular replacement / Resolution: 3.5109 Å

Authors

Emptage, R.P. / Tonthat, N.K. / York, J.D. / Schumacher, M.A. / Zhou, P.

Citation

Journal: J.Biol.Chem. / Year: 2014
Title: Structural Basis of Lipid Binding for the Membrane-embedded Tetraacyldisaccharide-1-phosphate 4'-Kinase LpxK.
Authors: Emptage, R.P. / Tonthat, N.K. / York, J.D. / Schumacher, M.A. / Zhou, P.

History

Deposition	Jul 8, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 9, 2014	Provider: repository / Type: Initial release
Revision 1.1	Jul 30, 2014	Group: Database references
Revision 1.2	Sep 17, 2014	Group: Database references
Revision 1.3	Sep 24, 2014	Group: Database references
Revision 1.4	Oct 25, 2017	Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.5	Feb 28, 2024	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 / struct_conn / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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 / _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	4lkv.cif.gz	518.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4lkv.ent.gz	438.1 KB	Display	PDB format
PDBx/mmJSON format	4lkv.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4lkv_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	4lkv_full_validation.pdf.gz	1.5 MB	Display
Data in XML	4lkv_validation.xml.gz	44.1 KB	Display
Data in CIF	4lkv_validation.cif.gz	58.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lk/4lkv ftp://data.pdbj.org/pub/pdb/validation_reports/lk/4lkv	HTTPS FTP

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Related structure data

Related structure data	4ehw 4ehx 4ehy 4itl 4itm 4itn
Similar structure data	4e8f-1 5vdu-2 6mjw-d 5o9t-2 5bud-2 5vdp-1 5vdq-1 3qz9-2 5vdv-2 5vdt-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Tetraacyldisaccharide 4'-kinase

B: Tetraacyldisaccharide 4'-kinase

C: Tetraacyldisaccharide 4'-kinase

D: Tetraacyldisaccharide 4'-kinase

hetero molecules

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

1

A: Tetraacyldisaccharide 4'-kinase

hetero molecules

defined by author&software
Evidence: gel filtration
38.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Tetraacyldisaccharide 4'-kinase

defined by author&software
Evidence: gel filtration
36.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Tetraacyldisaccharide 4'-kinase

hetero molecules

defined by author&software
Evidence: gel filtration
38 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Tetraacyldisaccharide 4'-kinase

defined by author&software
Evidence: gel filtration
36.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	136.632, 140.691, 173.846
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Noncrystallographic symmetry (NCS)

NCS domain: (Details: chain D) / NCS domain segments: (Selection details: chain 'D')

Details

Estimated from size exclusion chromatography and asymmetric unit of entries 4EHW, 4EHX, and 4EHY.

#1: Protein	Tetraacyldisaccharide 4'-kinase / Lipid A 4'-kinase Mass: 36597.730 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: lpxK, aq_1656 / Production host: Escherichia coli (E. coli) References: UniProt: O67572, tetraacyldisaccharide 4'-kinase
#2: Chemical	ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈N₂O₄S / Comment: pH buffer*YM
#3: Chemical	ChemComp-LP4 / 2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-4-O-phosphono-beta-D-glucopyranose Mass: 711.861 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃₄H₆₆NO₁₂P
#4: Chemical	ChemComp-LP5 / (R)-((2R,3S,4R,5R,6R)-3-HYDROXY-2-(HYDROXYMETHYL)-5-((R)-3-HYDROXYTETRADECANAMIDO)-6-(PHOSPHONOOXY)TETRAHYDRO-2H-PYRAN-4-YL) 3-HYDROXYTETRADECANOATE Mass: 711.861 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃₄H₆₆NO₁₂P
Nonpolymer details	LIPID IVa is represented by LP4 AND LP5

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.85 Å³/Da / Density % sol: 56.89 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: HEPES, MPD, lipid IVa, Tris, Triton X-100, DDM, NaCl, MgCl2, ADP, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 22-ID / Wavelength: 1 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 23, 2012

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 3.5→50 Å / Num. all: 21311 / Num. obs: 20053 / % possible obs: 94.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Diffraction-ID	% possible all
3.5-3.56	5.7	0.687	2	1	74.2
3.56-3.63	6.9	0.663	2.4	1	77.3
3.63-3.69	8.5	0.561	3.4	1	78.6
3.69-3.77	9.1	0.508	3.8	1	83.7
3.77-3.85	10.5	0.461	5	1	84.5
3.85-3.94	11.1	0.408	6	1	90.1
3.94-4.04	11.9	0.382	6.9	1	96.3
4.04-4.15	12.7	0.345	8.5	1	99.6
4.15-4.27	13.9	0.268	12.3	1	100
4.27-4.41	14.6	0.218	15.5	1	100
4.41-4.57	14.9	0.168	19.1	1	100
4.57-4.75	15.1	0.144	21.8	1	100
4.75-4.97	15	0.142	21.7	1	100
4.97-5.23	15	0.135	22.9	1	100
5.23-5.55	14.9	0.129	23.9	1	100
5.55-5.98	14.8	0.118	24.2	1	100
5.98-6.58	14.8	0.1	25.9	1	100
6.58-7.53	14.7	0.086	26.9	1	100
7.53-9.48	14.3	0.081	26.6	1	100
9.48-50	12.4	0.089	22.4	1	96.9

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHASER		phasing
RESOLVE		phasing
PHENIX	1.8.4_1496	refinement
PDB_EXTRACT	3.11	data extraction
SERGUI		data collection

Refinement

Resolution: 3.5109→39.51 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.51 / σ(F): 0.17 / Phase error: 33.5 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.3305	1790	9.99 %
R_work	0.2667	-	-
obs	0.273	17918	84.34 %

Solvent computation

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

Displacement parameters

B_iso mean: 185.5541 Å²

Refinement step

Cycle: LAST / Resolution: 3.5109→39.51 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10257	0	109	0	10366

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	10592
X-RAY DIFFRACTION	f_angle_d	0.833	14250
X-RAY DIFFRACTION	f_dihedral_angle_d	13.24	4107
X-RAY DIFFRACTION	f_chiral_restr	0.038	1559
X-RAY DIFFRACTION	f_plane_restr	0.004	1786

Refine LS restraints NCS

Number: 6212 / Type: POSITIONAL / Rms dev position: 8.986 Å

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 (%)
3.5109-3.6058	0.3973	59	0.3262	548	X-RAY DIFFRACTION	38
3.6058-3.7118	0.4044	82	0.3343	800	X-RAY DIFFRACTION	55
3.7118-3.8315	0.3823	108	0.3151	957	X-RAY DIFFRACTION	66
3.8315-3.9683	0.4152	126	0.3083	1057	X-RAY DIFFRACTION	73
3.9683-4.1271	0.36	131	0.2906	1156	X-RAY DIFFRACTION	80
4.1271-4.3147	0.3108	145	0.2764	1329	X-RAY DIFFRACTION	91
4.3147-4.5418	0.3048	162	0.2646	1427	X-RAY DIFFRACTION	97
4.5418-4.8259	0.2936	154	0.2429	1431	X-RAY DIFFRACTION	98
4.8259-5.1978	0.3251	170	0.2505	1449	X-RAY DIFFRACTION	98
5.1978-5.7195	0.3778	161	0.2743	1469	X-RAY DIFFRACTION	99
5.7195-6.5439	0.3939	160	0.3087	1483	X-RAY DIFFRACTION	99
6.5439-8.2323	0.3361	161	0.2778	1500	X-RAY DIFFRACTION	100
8.2323-39.5123	0.2584	171	0.2052	1522	X-RAY DIFFRACTION	98

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	0.054	-0.0147	0.087	0.0069	-0.0328	0.1451	-0.2337	0.09	0.3471	-0.0985	-0.2026	-0.1159	-0.3003	-0.1415	-1.2612	0.3782	0.2283	-0.1905	0.1769	0.1555	0.4117	-56.1398	-7.3224	-34.7332
2	0.6072	0.055	-0.1958	0.6723	0.4233	0.3704	-0.2274	-0.2076	0.1308	0.1718	-0.1936	-0.1555	-0.0548	-0.0729	-1.4494	0.2864	0.0913	-0.1347	0.3929	0.0906	0.082	-53.4395	-12.2966	-14.753
3	0.6063	-0.0347	0.2589	0.4326	-0.3058	0.6645	-0.4692	-0.1868	0.2618	0.1666	-0.3672	-0.4204	-0.0424	0.139	-4.9141	-0.345	0.4056	0.0685	0.2953	0.241	0.0942	-52.2473	-12.1031	-21.9327
4	0.2592	0.1239	-0.0424	0.1349	0.0885	0.3381	0.0334	0.007	-0.228	0.0608	0.1874	0.0098	0.3772	0.1881	0.1657	0.1302	0.2344	-0.3334	0.7285	0.4741	0.8635	-44.1748	-32.1921	-15.9117
5	0.9047	-0.4468	-0.0184	0.2385	0.0775	0.1664	-0.0202	-0.2489	-0.5297	0.0563	-0.1085	0.1741	0.1343	-0.0957	-0.7012	0.2378	0.0688	-0.3069	0.615	0.2887	0.9226	-49.663	-27.8909	-13.6057
6	0.0105	0.0242	-0.0142	0.2141	-0.2352	0.91	-0.0094	0.0551	-0.2144	-0.0523	-0.1221	0.0891	0.4743	-0.213	-0.4195	0.2516	-0.1414	0.087	-0.0437	-0.2948	0.7928	-10.1635	-57.921	-35.9536
7	0.061	-0.1657	0.0866	0.5145	-0.1502	0.295	-0.1636	0.0173	0.0514	0.2164	-0.2107	-0.0055	-0.1485	0.1372	-0.6507	0.2717	-0.3753	0.2278	0.4381	-0.1817	0.7914	-12.6376	-51.8261	-16.1243
8	0.0161	0.0476	0.0243	0.1698	0.0794	0.0346	-0.0634	-0.0761	-0.1532	0.2843	-0.0107	0.2386	0.1115	-0.0466	-0.0881	0.4249	-0.0132	0.0694	0.0732	-0.0435	0.6135	-5.8371	-53.7141	-11.8167
9	0.0172	-0.0427	-0.0409	0.1371	0.1003	0.0847	0.0644	0.3156	-0.3538	0.0321	-0.2372	0.4986	0.0466	-0.3775	-0.0529	0.1501	-0.2751	-0.0153	0.1694	-0.6204	0.6242	-18.7177	-47.6198	-27.1284
10	0.1079	-0.0227	-0.0697	0.0064	0.0191	0.0487	-0.0191	0.0549	0.0505	-0.0152	0.0221	0.0245	-0.0218	0.0123	0.0875	0.1022	-0.1652	0.0825	0.2804	-0.3151	0.312	-10.3823	-26.1424	-21.9355
11	0.7079	-0.1348	0.1356	0.3849	0.0448	0.321	0.0128	-0.0731	-0.2697	0.2307	-0.0979	0.1521	0.0453	-0.2259	0.0225	0.1304	-0.1629	0.0609	0.3633	-0.3657	0.4539	-11.2459	-37.0716	-16.5079
12	0.0099	-0.0448	0.077	0.1815	-0.3095	0.5473	0.0956	0.0345	-0.3314	-0.1279	0.082	0.5373	0.0917	-0.2567	0.1308	0.2573	0.0587	-0.1162	0.211	-0.0315	0.5641	-24.5057	22.2069	-3.8299
13	0.2711	-0.0071	0.0385	0.0008	0.006	0.0105	-0.0024	0.2022	-0.0229	-0.3866	0.1149	0.0973	0.0688	-0.0561	0.588	1.2252	-0.4478	-0.2201	0.2895	-0.1238	0.0447	-20.4302	9.5667	-23.8425
14	0.1339	-0.0601	-0.0467	0.0431	0.1162	0.5658	-0.051	0.1364	0.0519	-0.2704	-0.0614	-0.025	-0.1795	-0.0819	-0.3305	1.7115	-0.3379	0.0269	0.6175	-0.0949	0.1425	-17.9831	14.1359	-34.2292
15	0.1122	0.0635	-0.1605	0.0774	-0.1109	0.2235	0.0746	-0.0551	-0.0385	0.0173	0.2797	0.2062	0.2511	0.0615	2.3327	1.3543	-0.1418	-0.2435	0.1449	0.2194	-0.235	-18.1477	8.1083	-11.9281
16	1.1256	-0.0513	0.3661	0.0967	0.3825	1.9855	0.0643	0.4112	-0.0933	-0.2934	0.3165	-0.4015	-0.339	0.8122	-0.0322	0.8736	-0.0614	0.0761	0.4103	-0.2213	0.3038	3.6858	5.1352	-24.8646
17	0.0111	0.0055	0.0015	0.0171	-0.0078	0.0039	-0.0883	-0.0039	0.1068	-0.0497	0.0583	0.1318	0.0111	0.0023	-0	1.1701	-0.0579	-0.1181	1.0989	-0.2718	1.542	5.2897	18.4295	-18.8111
18	0.0217	0.0104	0.0226	0.0062	0.015	0.0276	-0.2146	0.3228	0.1902	-0.1539	0.0217	0.0183	-0.0211	-0.4069	0.0091	0.6408	-0.2978	-0.3941	1.3517	0.2719	1.2852	5.6171	25.6312	-26.6905
19	0.3999	-0.0208	0.1332	0.4346	-0.2811	0.216	0.2322	0.4026	0.3105	-0.6007	0.3629	-0.2864	-0.3992	0.5726	0.1494	1.1194	-0.2884	0.4273	0.7243	-0.2738	0.9452	-3.798	7.1171	-27.0936
20	0.0129	-0.0158	0.0108	-0.0315	0.0135	0.0014	-0.2546	-0.4317	0.1103	0.5634	-0.1883	0.518	0.4512	0.0956	-1.1852	1.0198	0.7888	1.204	0.7244	-0.4422	0.688	-36.1475	-26.2055	-62.7862
21	0.2659	-0.0457	0.0402	0.0167	-0.0215	0.0469	0.0776	0.1704	0.142	-0.1134	-0.237	0.0123	-0.0538	-0.0294	-0.2767	0.5223	0.2066	0.3176	0.4351	0.0482	0.5988	-33.986	-14.3567	-75.8878
22	0.1512	0.0948	0.1572	0.2914	-0.1	0.301	0.0475	-0.255	0.079	0.0221	0.0348	0.1603	-0.085	0.0703	0.3132	0.7098	0.238	0.3482	0.7445	-0.2321	0.6848	-21.2199	-10.6826	-57.8599
23	0.0404	0.0085	-0.0119	0.0248	-0.0243	0.0228	0.1584	-0.2452	0.2193	0.1081	0.2593	0.0546	-0.1307	0.3022	0	0.7801	-0.0045	0.1792	0.5547	-0.0253	0.709	-7.5692	-17.0779	-61.1806
24	0.1096	0.0172	-0.0813	0.0937	-0.0036	0.0648	-0.0499	-0.3263	-0.0616	0.2129	-0.0176	0.1179	0.0725	0.0301	0.1791	0.3776	0.2064	0.2496	1.0928	-0.0848	0.3657	-8.7252	-25.2858	-53.6399
25	0.4989	0.0592	-0.0209	0.0699	-0.0814	0.1175	0.1129	0.1054	0.2515	0.1006	-0.1934	0.4832	-0.1178	-0.232	-0.1173	1.0683	0.4121	0.1999	0.8061	-0.2636	1.06	-34.4234	-8.5216	-60.9394

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 50 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 51 through 80 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 81 through 199 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 200 through 248 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 249 through 315 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 3 through 50 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 51 through 80 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 81 through 129 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 130 through 222 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 223 through 248 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 249 through 315 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 2 through 25 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 26 through 80 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 81 through 129 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 130 through 199 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 200 through 228 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 229 through 248 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 249 through 267 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 268 through 315 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 2 through 173 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 174 through 199 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 200 through 221 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 222 through 248 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 249 through 290 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 291 through 315 )

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