PDB-5b58: Inward-facing conformation of ABC heme importer BhuUV in complex ...

ID or keywords:

Entry

Database: PDB / ID: 5b58

Title

Inward-facing conformation of ABC heme importer BhuUV in complex with periplasmic heme binding protein BhuT from Burkholderia cenocepacia

Components

Hemin import ATP-binding protein HmuV
Putative hemin ABC transport system, membrane protein
Putative hemin transport system, substrate-binding protein

Keywords

METAL BINDING PROTEIN / metal-binding

Function / homology

Function and homology information

siderophore-iron import into cell / transmembrane transporter activity / ATP hydrolysis activity / ATP binding / metal ion binding / plasma membrane
Similarity search - Function

Biological species

Burkholderia cenocepacia J2315 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.21 Å

Model details

Bacterial heme transporter BhuUV-T

Authors

Naoe, Y. / Nakamura, N. / Doi, A. / Shiro, Y. / Sugimoto, H.

Funding support

Japan, 4items

Citation

Journal: Nat Commun / Year: 2016
Title: Crystal structure of bacterial haem importer complex in the inward-facing conformation
Authors: Naoe, Y. / Nakamura, N. / Doi, A. / Sawabe, M. / Nakamura, H. / Shiro, Y. / Sugimoto, H.

History

Deposition	Apr 25, 2016	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Nov 23, 2016	Provider: repository / Type: Initial release
Revision 1.1	Feb 26, 2020	Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2	Nov 8, 2023	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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PDBx/mmCIF format	5b58.cif.gz	532.5 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	5b58_validation.pdf.gz	478.4 KB	Display	wwPDB validaton report
Full document	5b58_full_validation.pdf.gz	526.5 KB	Display
Data in XML	5b58_validation.xml.gz	52.4 KB	Display
Data in CIF	5b58_validation.cif.gz	71.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b5/5b58 ftp://data.pdbj.org/pub/pdb/validation_reports/b5/5b58	HTTPS FTP

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Related structure data

Related structure data	5b57C 2qi9S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4dbl-1 4dbl-2 2qi9-d 6so5-d 4fi3-d 3fdu-d 4q4a-d 3qf4-d 3761 4wcz-d 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 (5) #220 - Apr 2018 Dehalogenases similarity (2) #95 - Nov 2007 Multidrug Resistance Transporters similarity (5) #111 - Mar 2009 Hydrogenase similarity (2)

Deposited unit

A: Putative hemin ABC transport system, membrane protein

B: Putative hemin ABC transport system, membrane protein

C: Hemin import ATP-binding protein HmuV

D: Hemin import ATP-binding protein HmuV

T: Putative hemin transport system, substrate-binding protein

164 kDa, 5 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)	69.016, 99.751, 253.496
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Putative hemin ABC transport system, membrane protein / heme importer transmembrane subunit BhuU Mass: 38801.512 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia cenocepacia J2315 (bacteria) Strain: J2315 / Gene: hmuU, BCAM2629 / Plasmid: pET-19b / Production host: Escherichia coli (E. coli) / Strain (production host): c41(DE3) / References: UniProt: B4EKB4
#2: Protein	Hemin import ATP-binding protein HmuV / heme importer ATP-binding subunit BhuV Mass: 29232.479 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia cenocepacia J2315 (bacteria) Strain: J2315 / Gene: hmuV, BCAM2630 / Plasmid: pET-19b / Production host: Escherichia coli (E. coli) / Strain (production host): c41(DE3) References: UniProt: B4EKB5, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances
#3: Protein	Putative hemin transport system, substrate-binding protein / periplasmic heme-binding protein BhuT Mass: 28016.029 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia cenocepacia J2315 (bacteria) Strain: J2315 / Gene: hmuT, BCAM2628 / Plasmid: pGEX6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: B4EKB3

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.66 Å³/Da / Density % sol: 53.74 % / Mosaicity: 1.267 °
Crystal grow	Temperature: 293 K / Method: vapor diffusion / pH: 7.6 / Details: 15% PEG 2000, 0.1M HEPES

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SPring-8

/ Beamline: BL41XU / Wavelength: 1 Å

Detector

Type: RAYONIX MX225HE / Detector: CCD / Date: Feb 1, 2012 / Details: mirrors

Radiation

Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 3.2→50 Å / Num. obs: 28840 / % possible obs: 96.9 % / Redundancy: 3.9 % / B_iso Wilson estimate: 61.77 Å² / R_merge(I) obs: 0.092 / R_pim(I) all: 0.048 / R_rim(I) all: 0.105 / Χ²: 0.888 / Net I/av σ(I): 10 / Net I/σ(I): 7.1 / Num. measured all: 111437

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
3.2-3.26	2.5	0.438	1357	0.081	0.307	0.539	0.734	92.6
3.26-3.31	2.6	0.422	1352	0.101	0.293	0.517	0.739	93.2
3.31-3.38	2.8	0.399	1358	0.193	0.267	0.484	0.794	93.6
3.38-3.45	2.9	0.377	1422	0.318	0.244	0.452	0.794	95.4
3.45-3.52	3	0.369	1371	0.381	0.238	0.443	0.815	95.6
3.52-3.6	3.2	0.331	1425	0.512	0.203	0.391	0.854	96.3
3.6-3.69	3.3	0.311	1429	0.603	0.187	0.366	0.918	96.8
3.69-3.79	3.4	0.301	1401	0.658	0.179	0.353	0.899	96.2
3.79-3.91	3.4	0.286	1413	0.742	0.17	0.335	0.932	96.2
3.91-4.03	3.6	0.239	1450	0.836	0.138	0.278	0.934	97.4
4.03-4.18	3.9	0.203	1427	0.891	0.111	0.233	0.972	97.7
4.18-4.34	4.1	0.169	1449	0.941	0.089	0.192	0.948	98
4.34-4.54	4.3	0.144	1440	0.951	0.074	0.162	0.978	98.2
4.54-4.78	4.5	0.121	1476	0.97	0.061	0.135	0.914	98.9
4.78-5.08	4.3	0.113	1453	0.971	0.058	0.127	0.851	98.2
5.08-5.47	4.5	0.103	1478	0.979	0.051	0.116	0.834	97.9
5.47-6.02	4.4	0.102	1483	0.974	0.051	0.115	0.746	99
6.02-6.89	4.7	0.081	1509	0.986	0.04	0.091	0.753	98.8
6.89-8.67	5.3	0.053	1544	0.997	0.024	0.059	0.926	99.4
8.67-50	5.9	0.045	1603	0.997	0.02	0.049	1.07	97.2

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
HKL-2000		data scaling
PDB_EXTRACT	3.2	data extraction
PHASER	2.5.1	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2QI9

2qi9

Resolution: 3.21→32.612 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 30.95 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.3095	1066	4.75 %	Ramdom selection
R_work	0.2691	21356	-	-
obs	0.271	22422	76.14 %	-

Solvent computation

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

Displacement parameters

B_iso max: 264.62 Å² / B_iso mean: 72.8637 Å² / B_iso min: 6.73 Å²

Refinement step

Cycle: final / Resolution: 3.21→32.612 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10446	0	0	0	10446
Num. residues	-	-	-	-	1438

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	10626
X-RAY DIFFRACTION	f_angle_d	1.082	14495
X-RAY DIFFRACTION	f_chiral_restr	0.051	1778
X-RAY DIFFRACTION	f_plane_restr	0.006	1866
X-RAY DIFFRACTION	f_dihedral_angle_d	15.679	6336

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
3.21-3.356	0.2782	11	0.3037	148	159	4
3.356-3.5327	0.2944	46	0.2891	1036	1082	30
3.5327-3.7537	0.3719	137	0.2943	2796	2933	81
3.7537-4.0431	0.3645	152	0.2843	3357	3509	96
4.0431-4.449	0.3056	170	0.2496	3397	3567	98
4.449-5.0907	0.2981	172	0.2419	3445	3617	98
5.0907-6.4058	0.299	191	0.298	3498	3689	99
6.4058-32.6134	0.282	187	0.2607	3679	3866	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	0.4685	0.2918	-0.1203	0.2078	-0.0679	0.4608	0.1266	-0.0478	-0.3405	0.9344	-0.2395	-0.3171	0.2249	0.0493	-0.1179	1.3307	0.1663	-0.1334	0.4359	0.1998	0.7298	13.8521	-32.1071	46.2149
2	0.1797	-0.0565	-0.1272	0.19	0.1356	0.2816	-0.2262	-0.1184	-0.2149	0.3876	-0.0681	0.1138	-0.087	-0.1696	-0.7416	0.7101	0.085	0.1665	0.528	0.027	0.3741	3.2193	-4.4111	43.1515
3	0.1721	0.1087	-0.2996	1.1469	-0.0762	0.567	-0.211	-0.2318	-0.3718	0.4929	-0.1007	0.1897	0.3474	0.2724	-0.9894	0.5776	0.1251	0.1326	0.3836	0.1254	0.4522	6.4492	-15.4594	33.3621
4	0.5349	0.1356	0.0148	0.0314	0.0044	-0.0001	-0.099	-0.6461	-0.0672	0.1637	0.072	-0.0541	0.004	0.0856	0.0347	0.4336	0.2224	-0.0949	0.349	-0.1303	0.3954	9.5293	32.7859	27.1233
5	0.0247	-0.0059	-0.0928	-0.0001	0.008	0.3754	-0.0546	0.0078	0.0462	0.0632	-0.0588	0.0327	0.1214	0.0725	-0.1725	1.0972	-0.2692	-0.423	0.9911	-0.5518	0.67	21.4456	38.6748	55.3263
6	0.1019	-0.0679	0.07	0.102	-0.0278	0.0458	-0.0465	-0.2689	0.0647	0.0571	0.0523	-0.0545	-0.0827	0.0593	0.0107	0.0832	-0.0444	-0.0166	0.534	-0.1015	-0.1281	21.9527	13.2671	36.8251
7	0.1219	0.046	-0.0497	0.0493	0.0125	0.0359	-0.0111	0.2981	-0.1133	-0.0735	-0.1542	-0.0344	-0.1207	-0.0143	-0.1652	0.2149	-0.0125	-0.2426	0.783	0.2549	0.4831	30.7175	4.0646	29.3884
8	0.0708	-0.0184	-0.027	0.0753	0.0732	0.1307	-0.0358	-0.0253	0.0052	0.2086	0.0066	-0.0045	0.0317	0.0355	-0.1493	0.5846	0.1269	-0.1612	0.931	-0.006	0.3681	22.9349	6.4188	43.8182
9	0.1797	-0.0786	-0.0086	0.0497	0.0143	0.0178	0.0721	-0.2504	0.1925	-0.0097	0.1109	-0.1185	0.0064	0.0562	-0.0517	0.1778	-0.0107	0.2361	0.1667	-0.101	0.1959	23.5712	17.1222	16.2833
10	0.0615	0.0396	-0.0866	0.1067	-0.0366	0.1317	-0.0819	-0.1897	0.0584	-0.0079	-0.1268	-0.2023	-0.1125	0.193	-0.4753	0.0242	-0.3441	-0.2576	0.5818	-0.1036	0.0925	19.3014	15.3953	27.7298
11	0.1673	0.1619	0.0835	0.3314	0.079	0.1005	-0.0645	-0.2359	0.0057	0.2748	-0.191	0.0064	-0.0441	-0.1264	-0.2231	0.1124	0.084	-0.2844	0.4599	-0.2779	0.2168	7.4636	19.0435	36.692
12	1.1269	0.1983	-0.477	0.8745	-0.5874	0.8753	0.2808	-0.3494	0.4309	0.2804	0.1948	-0.0567	-0.3019	0.0875	0.6676	0.4101	0.0151	-0.2712	0.4332	-0.3414	1.0365	-18.0217	0.8012	-0.7022
13	0.0253	-0.028	0.0408	0.0487	-0.0384	0.1194	0.0268	-0.0729	0.0006	-0.0095	-0.0938	0.3187	0.1245	0.082	-0.0808	0.2491	-0.0195	0.1085	0.3435	-0.2287	0.8407	-14.1127	-7.8518	9.2488
14	0.1103	-0.0367	-0.0315	0.0662	0.021	0.0772	0.0043	0.1205	-0.0679	-0.0469	-0.3211	-0.0639	0.1082	-0.0032	-0.4255	0.4594	0.0105	0.2117	0.079	-0.2	0.4863	-0.4416	-22.5248	6.7624
15	0.0838	-0.0731	-0.086	0.103	0.1232	0.0925	-0.0282	0.3503	-0.2343	-0.1459	-0.2553	0.3336	0.0156	-0.2348	-0.6853	0.4243	0.2617	-0.2706	-0.1792	-0.9502	0.5165	-8.5165	-6.7096	-10.7551
16	0.1578	0.0145	-0.0704	0.1505	0.0165	0.0428	0.0158	-0.2075	-0.1072	-0.2283	-0.0202	-0.1171	-0.0122	0.0447	-0.0275	0.1313	0.0227	0.1319	0.2022	-0.0638	0.1935	26.351	-1.0407	-7.0704
17	0.1208	0.0386	0.1366	0.4825	-0.0359	0.3919	-0.0611	-0.1091	-0.0619	-0.0119	0.2962	-0.2982	-0.0709	-0.2009	0.5871	-0.077	0.1399	0.0796	-0.1297	-0.1481	0.1747	21.9999	13.827	1.4469
18	0.7084	-0.5526	0.3101	0.6858	-0.1251	1.1429	-0.0097	-0.2059	0.2147	-0.0273	-0.1187	0.0617	-0.3015	-0.3956	-0.4633	0.2197	0.006	0.0334	0.2431	-0.0794	0.1745	11.9964	19.1104	-1.4169
19	0.2306	-0.1176	-0.1066	0.0696	0.0484	0.0561	-0.0185	0.5513	-0.1198	-0.2393	-0.3174	-0.12	-0.1204	0.0557	-0.3859	0.6971	0.0381	0.1589	0.1279	-0.3744	-0.256	11.9817	1.4718	-17.7967
20	0.0897	0.0653	0.0904	0.059	0.0487	0.0956	-0.3647	-0.2798	-0.1825	0.8425	0.0632	-0.0373	0.6556	1.126	0.2329	2.0536	0.4183	0.1418	1.5264	0.2412	0.673	19.0636	-11.3513	73.3607
21	0.8373	-0.2522	0.1387	0.2847	0.1714	0.286	-0.0328	-0.0588	-0.0203	0.7409	0.1413	-0.3366	0.344	1.0501	0.1838	1.771	-0.0598	-0.3399	1.7277	-0.1011	0.3494	22.8747	14.2982	73.1294

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 22 through 80 )	A	22 - 80
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 81 through 218 )	A	81 - 218
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 219 through 359 )	A	219 - 359
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 22 through 48 )	B	22 - 48
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 49 through 80 )	B	49 - 80
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 81 through 145 )	B	81 - 145
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 146 through 172 )	B	146 - 172
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 173 through 226 )	B	173 - 226
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 227 through 259 )	B	227 - 259
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 260 through 303 )	B	260 - 303
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 304 through 359 )	B	304 - 359
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 1 through 39 )	C	1 - 39
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 40 through 99 )	C	40 - 99
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 100 through 163 )	C	100 - 163
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 164 through 273 )	C	164 - 273
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 1 through 64 )	D	1 - 64
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 65 through 108 )	D	65 - 108
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 109 through 187 )	D	109 - 187
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 188 through 273 )	D	188 - 273
20	X-RAY DIFFRACTION	20	chain 'T' and (resid 41 through 151 )	T	41 - 151
21	X-RAY DIFFRACTION	21	chain 'T' and (resid 152 through 305 )	T	152 - 305

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