PDB-5hno: The structure of the kdo-capped saccharide binding subunit of the...

ID or keywords:

Entry

Database: PDB / ID: 5hno

Title

The structure of the kdo-capped saccharide binding subunit of the O-12 specific ABC transporter, Wzt

Components

ABC type transport system putative ATP binding protein

Keywords

TRANSPORT PROTEIN / O antigen export /

carbohydrate binding subunit /

ABC transporter

Function / homology

Function and homology information

Biological species

Raoultella terrigena (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.7 Å

Authors

Mallette, E. / Mann, E. / Whitfield, C. / Kimber, M.S.

Citation

Journal: J.Biol.Chem. / Year: 2016
Title: The Klebsiella pneumoniae O12 ATP-binding Cassette (ABC) Transporter Recognizes the Terminal Residue of Its O-antigen Polysaccharide Substrate.
Authors: Mann, E. / Mallette, E. / Clarke, B.R. / Kimber, M.S. / Whitfield, C.

History

Deposition	Jan 18, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 9, 2016	Provider: repository / Type: Initial release
Revision 1.1	Mar 16, 2016	Group: Database references
Revision 1.2	May 11, 2016	Group: Database references
Revision 1.3	Jul 6, 2016	Group: Other
Revision 1.4	Mar 6, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5hno.cif.gz	298.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5hno.ent.gz	250.3 KB	Display	PDB format
PDBx/mmJSON format	5hno.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

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

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Related structure data

Related structure data	5hnpC C: citing same article (ref.)
Similar structure data	5fpi-d 4qb7-d 5hnp-d 6yz5-d 4m6d-3 4nxi-d 4q98-d 7c8w-d 4ckt-d 7b14-d 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#123 - Mar 2010 P-glycoprotein similarity (3) #95 - Nov 2007 Multidrug Resistance Transporters similarity (3)

Deposited unit

A: ABC type transport system putative ATP binding protein

B: ABC type transport system putative ATP binding protein

C: ABC type transport system putative ATP binding protein

hetero molecules

62.6 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: ABC type transport system putative ATP binding protein

B: ABC type transport system putative ATP binding protein

hetero molecules

defined by author&software
41.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: ABC type transport system putative ATP binding protein

hetero molecules

C: ABC type transport system putative ATP binding protein

hetero molecules

defined by author&software
41.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	141.750, 53.550, 87.470
Angle α, β, γ (deg.)	90.00, 125.77, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	B-526- HOH

#1: Protein	ABC type transport system putative ATP binding protein Mass: 20855.514 Da / Num. of mol.: 3 / Fragment: unp reisdues 268-442 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Raoultella terrigena (bacteria) / Gene: wzt / Plasmid: pWQ284 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(pEEM003) / References: UniProt: Q6U8B1
#2: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.15 Å³/Da / Density % sol: 42.86 % Description: Crystals grew as small plates up to 50 micrometers in width.
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M Na HEPESm 0.8 M Na phosphate, 0.8 M K Phosphate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.03322 Å
Detector	Type: RAYONIX MX-300 / Detector: CCD / Date: May 7, 2015 Details: ultra-low expansion (ULE) titanium siliicate flat mirror
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.03322 Å / Relative weight: 1
Reflection	Resolution: 1.7→40 Å / Num. obs: 58678 / % possible obs: 99.5 % / Redundancy: 3.7 % / B_iso Wilson estimate: 28 Å² / CC_1/2: 0.8 / R_sym value: 0.035 / Net I/σ(I): 19.93
Reflection shell	Resolution: 1.7→1.74 Å / R_merge(I) obs: 0.88 / Mean I/σ(I) obs: 1.87 / % possible all: 99.4

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XDS		data reduction
XSCALE		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.7→35.487 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.92 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2155	2932	5 %
R_work	0.1831	-	-
obs	0.1846	58637	99.72 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.7→35.487 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3813	0	2	276	4091

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	3907
X-RAY DIFFRACTION	f_angle_d	0.921	5268
X-RAY DIFFRACTION	f_dihedral_angle_d	13.69	1489
X-RAY DIFFRACTION	f_chiral_restr	0.032	601
X-RAY DIFFRACTION	f_plane_restr	0.003	678

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 (%)
1.7-1.7279	0.3951	141	0.3872	2668	X-RAY DIFFRACTION	99
1.7279-1.7577	0.3439	136	0.335	2603	X-RAY DIFFRACTION	99
1.7577-1.7896	0.337	138	0.314	2625	X-RAY DIFFRACTION	99
1.7896-1.824	0.3	138	0.2723	2627	X-RAY DIFFRACTION	100
1.824-1.8613	0.2696	139	0.2575	2628	X-RAY DIFFRACTION	100
1.8613-1.9017	0.2686	139	0.2436	2631	X-RAY DIFFRACTION	100
1.9017-1.946	0.2735	138	0.2391	2652	X-RAY DIFFRACTION	100
1.946-1.9946	0.2697	139	0.2235	2638	X-RAY DIFFRACTION	100
1.9946-2.0486	0.2622	139	0.2272	2639	X-RAY DIFFRACTION	100
2.0486-2.1088	0.2637	138	0.2111	2622	X-RAY DIFFRACTION	100
2.1088-2.1769	0.2412	141	0.2058	2671	X-RAY DIFFRACTION	100
2.1769-2.2547	0.2171	138	0.1952	2617	X-RAY DIFFRACTION	100
2.2547-2.3449	0.1993	140	0.1957	2671	X-RAY DIFFRACTION	100
2.3449-2.4516	0.2439	140	0.2037	2652	X-RAY DIFFRACTION	100
2.4516-2.5809	0.2329	139	0.2007	2637	X-RAY DIFFRACTION	100
2.5809-2.7425	0.2503	139	0.2039	2656	X-RAY DIFFRACTION	100
2.7425-2.9542	0.2213	141	0.2004	2680	X-RAY DIFFRACTION	100
2.9542-3.2513	0.2209	140	0.1907	2653	X-RAY DIFFRACTION	100
3.2513-3.7213	0.1969	142	0.1634	2687	X-RAY DIFFRACTION	100
3.7213-4.6867	0.1657	141	0.1298	2694	X-RAY DIFFRACTION	100
4.6867-35.4952	0.1711	146	0.1422	2754	X-RAY DIFFRACTION	99

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	5.9213	1.6406	3.2324	7.9529	2.9602	6.9013	-0.0559	0.5897	0.5285	-0.2028	-0.1048	0.2088	-0.0297	-0.5124	0.1534	0.293	-0.001	-0.0104	0.5843	0.1086	0.2449	31.7331	27.2895	34.7303
2	4.2136	0.3099	0.9715	1.618	0.1985	4.3187	-0.0377	0.2718	0.1456	-0.1331	0.0185	0.0264	0.1652	-0.4687	0.0236	0.1714	-0.0303	0.0312	0.2226	0.0303	0.1461	36.4357	19.53	49.5788
3	4.5579	2.7856	3.1381	2.3823	1.4183	8.4544	-0.208	0.9818	0.0323	-0.2913	0.3005	-0.2143	0.3553	0.2414	-0.1218	0.2139	-0.0045	0.0284	0.4044	0.0209	0.1944	40.9479	21.1616	40.67
4	6.0863	-1.5843	2.9345	3.3581	-1.1998	6.5044	-0.3016	-0.6747	0.4626	0.3995	0.0985	-0.1961	-0.305	-0.0613	0.2007	0.2075	-0.0167	0.0328	0.2259	-0.0354	0.2606	50.9963	24.6352	63.1771
5	5.6682	1.2657	2.7526	2.4934	1.7122	3.4314	0.4562	-0.803	-0.4521	0.3381	0.0369	-1.3108	0.3466	0.3096	-0.352	0.4329	-0.073	-0.2521	0.8156	0.269	1.3648	85.9981	17.8014	72.6129
6	7.4448	4.5646	5.94	5.4209	1.5312	6.4603	-0.4645	0.2397	-0.6924	-0.2005	-0.5725	-1.0165	0.3739	1.0859	0.683	0.2907	-0.0624	0.0247	0.6424	0.1917	1.0543	79.4105	18.4725	62.5309
7	5.8789	4.3205	-0.5359	5.9948	0.1598	5.3618	-0.2459	0.7041	-0.0178	0.1593	-0.0476	-0.9263	1.0724	0.8293	0.1238	0.4006	0.1208	0.0481	0.3811	0.2115	0.6379	67.4455	6.1651	67.0043
8	3.051	-3.5355	-1.8888	4.601	2.8445	2.0927	0.0549	-0.4008	-1.2011	0.103	-0.3268	0.2019	1.5119	0.7789	0.0663	0.5345	0.0643	0.0421	0.3143	0.1509	0.49	57.5779	5.3461	59.0377
9	5.9331	3.4428	3.8763	6.0318	3.8	6.8915	0.0896	-1.1059	-0.2886	0.8457	-0.5057	-0.9714	-0.2577	0.2266	0.285	0.4271	-0.0733	-0.1854	0.5881	0.2183	0.4886	70.3843	17.5792	75.3227
10	4.9888	1.1075	0.2572	8.1003	3.264	2.0467	0.1057	-0.1308	-0.0456	0.0775	-0.0847	-0.7489	0.2799	-0.1032	0.0416	0.2829	-0.0017	0.023	0.2595	0.0124	0.4477	65.4969	20.1519	63.4998
11	5.9657	0.2015	1.7896	4.8249	0.7932	4.4647	-0.1152	-0.2857	0.3465	0.3247	-0.6434	-0.5826	-0.5195	0.6719	0.4101	0.2516	-0.0478	-0.0026	0.285	0.1152	0.4092	64.5417	21.8501	68.7122
12	4.9057	0.0981	2.0758	3.184	0.2144	5.0088	0.0412	-0.4867	-0.4992	0.2368	-0.2217	-0.7532	0.0936	0.3372	-0.0247	0.2564	-0.0141	-0.0428	0.2542	0.142	0.4036	62.635	12.6804	66.8568
13	4.6259	2.4939	2.7506	4.6226	2.204	6.8203	0.0378	-0.1239	0.095	-0.0191	-0.1737	-0.6095	-0.3893	0.2978	0.1382	0.2898	-0.0094	0.0164	0.2595	0.0541	0.4343	68.9836	20.5542	64.2762
14	6.492	-5.0915	-2.7539	8.0765	0.7535	6.387	0.1051	-0.2983	0.9965	-0.2784	-0.1623	-0.3582	-1.4264	0.4174	0.1381	0.5784	-0.1873	-0.1969	0.5292	0.1775	0.9168	74.047	29.8629	70.5646
15	5.2389	5.5333	5.0722	6.6535	4.4624	6.4973	0.3164	0.0645	-0.196	0.1161	-0.2132	-0.404	0.4206	0.4884	-0.1733	0.3201	0.0729	0.0785	0.2546	0.0439	0.543	67.2257	11.6991	57.893
16	7.9852	-0.3281	0.0543	5.3282	-1.1509	4.6084	0.1324	0.3758	-1.4256	-0.2136	-0.1133	0.0413	0.6559	-0.2755	-0.0449	0.3374	-0.046	0.0254	0.2197	-0.0757	0.2868	42.5033	10.5521	51.4859
17	2.5393	-4.0965	1.4851	9.6968	0.3108	7.8547	0.0628	0.6409	0.4765	-0.7647	-0.3534	0.4012	-0.2888	-1.0433	0.2157	0.3862	-0.0483	-0.1206	0.574	-0.0098	0.3224	-5.9059	7.3707	44.9834
18	2.8532	-1.9905	-3.2765	4.8999	-0.0174	5.6902	0.1584	0.2456	-0.5095	-0.0824	-0.0603	-0.319	0.4735	-0.1458	-0.0082	0.2986	-0.0742	-0.0901	0.3453	-0.0565	0.3758	3.6461	2.491	51.4564
19	2.3324	2.2578	-0.8897	3.628	0.0483	3.1938	-0.2369	0.695	0.6209	-0.2622	0.3189	-0.1662	-0.609	0.2716	-0.1369	0.4486	-0.1168	-0.0685	0.4123	0.0816	0.3746	12.1882	17.4549	51.1796
20	8.3785	-0.4819	1.4453	0.8848	-0.7026	2.1868	-0.2149	0.516	0.3707	-0.2802	0.1065	0.0686	-0.395	0.233	0.1059	0.3157	-0.0413	-0.065	0.2714	0.0228	0.2384	12.4942	18.098	56.3528
21	2.1898	0.5582	3.4284	2.7326	-0.5939	6.7739	-0.2611	-0.3747	-0.277	0.0261	0.1786	0.217	0.1115	-0.5613	0.0767	0.1761	-0.0232	0.0058	0.2247	-0.0158	0.1833	4.7056	9.9663	61.9703
22	5.5865	0.5157	1.6055	1.9374	0.4256	3.4301	-0.4285	-0.0352	0.3598	-0.118	0.145	0.2855	-0.4704	-0.2449	0.2365	0.2502	0.0131	-0.0504	0.1769	0.0073	0.1893	5.7353	15.3495	59.9199
23	6.1451	-4.2618	-5.4519	6.4471	3.7423	4.9248	-0.2431	-0.8483	-0.3908	0.612	0.0168	0.4815	0.4238	-0.1166	0.0998	0.3342	-0.0848	-0.0148	0.4345	0.0551	0.3513	-3.3486	5.5922	61.2147
24	6.537	1.3884	2.6999	2.2845	-0.0039	3.1703	-0.2177	0.4179	0.0827	0.0934	0.0623	-0.1222	-0.3939	0.4839	0.1571	0.2315	-0.0482	0.0194	0.2782	0.0228	0.1946	25.8506	14.6767	65.7906

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 274:302 )	A	274 - 302
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 303:390 )	A	303 - 390
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 391:414 )	A	391 - 414
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 415:440 )	A	415 - 440
5	X-RAY DIFFRACTION	5	( CHAIN B AND RESID 275:287 )	B	275 - 287
6	X-RAY DIFFRACTION	6	( CHAIN B AND RESID 288:302 )	B	288 - 302
7	X-RAY DIFFRACTION	7	( CHAIN B AND RESID 303:321 )	B	303 - 321
8	X-RAY DIFFRACTION	8	( CHAIN B AND RESID 322:328 )	B	322 - 328
9	X-RAY DIFFRACTION	9	( CHAIN B AND RESID 329:344 )	B	329 - 344
10	X-RAY DIFFRACTION	10	( CHAIN B AND RESID 345:353 )	B	345 - 353
11	X-RAY DIFFRACTION	11	( CHAIN B AND RESID 354:375 )	B	354 - 375
12	X-RAY DIFFRACTION	12	( CHAIN B AND RESID 376:392 )	B	376 - 392
13	X-RAY DIFFRACTION	13	( CHAIN B AND RESID 393:402 )	B	393 - 402
14	X-RAY DIFFRACTION	14	( CHAIN B AND RESID 403:412 )	B	403 - 412
15	X-RAY DIFFRACTION	15	( CHAIN B AND RESID 413:422 )	B	413 - 422
16	X-RAY DIFFRACTION	16	( CHAIN B AND RESID 423:442 )	B	423 - 442
17	X-RAY DIFFRACTION	17	( CHAIN C AND RESID 274:287 )	C	274 - 287
18	X-RAY DIFFRACTION	18	( CHAIN C AND RESID 288:302 )	C	288 - 302
19	X-RAY DIFFRACTION	19	( CHAIN C AND RESID 303:321 )	C	303 - 321
20	X-RAY DIFFRACTION	20	( CHAIN C AND RESID 322:338 )	C	322 - 338
21	X-RAY DIFFRACTION	21	( CHAIN C AND RESID 339:362 )	C	339 - 362
22	X-RAY DIFFRACTION	22	( CHAIN C AND RESID 363:401 )	C	363 - 401
23	X-RAY DIFFRACTION	23	( CHAIN C AND RESID 402:414 )	C	402 - 414
24	X-RAY DIFFRACTION	24	( CHAIN C AND RESID 415:439 )	C	415 - 439

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Yorodumi