PDB-6iv2: Crystal structure of a bacterial Bestrophin homolog from Klebsiel...

ID or keywords:

Entry

Database: PDB / ID: 6iv2

Title

Crystal structure of a bacterial Bestrophin homolog from Klebsiella pneumoniae with a mutation Y211A

Components

Bestrophin homolog

Keywords

MEMBRANE PROTEIN / Bestrophin-1 / homolog / mutation / klebsiella pneumoniae

Function / homology

UPF0187 family / Bestrophin/UPF0187 / Bestrophin, RFP-TM, chloride channel / chloride channel activity / membrane / Ibestrophin

Function and homology information

Biological species

Klebsiella pneumoniae IS53 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.62 Å

Authors

Kittredge, A. / Chen, S. / Yang, T.

Funding support

China, 1items

Citation

Journal: Commun Biol / Year: 2019
Title: Dual Ca2+-dependent gates in human Bestrophin1 underlie disease-causing mechanisms of gain-of-function mutations.
Authors: Ji, C. / Kittredge, A. / Hopiavuori, A. / Ward, N. / Chen, S. / Fukuda, Y. / Zhang, Y. / Yang, T.

History

Deposition	Dec 2, 2018	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Nov 13, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jun 8, 2022	Group: Database references / Derived calculations / Structure summary Category: audit_author / database_2 ...audit_author / database_2 / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.2	May 29, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	6iv2_validation.pdf.gz	476.9 KB	Display	wwPDB validaton report
Full document	6iv2_full_validation.pdf.gz	507.7 KB	Display
Data in XML	6iv2_validation.xml.gz	47.9 KB	Display
Data in CIF	6iv2_validation.cif.gz	64.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/iv/6iv2 ftp://data.pdbj.org/pub/pdb/validation_reports/iv/6iv2	HTTPS FTP

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Related structure data

Related structure data	6iv0C 6iv1C 6iv3C 6iv4C 6ivjC 6ivkC 6ivlC 6ivmC 6ivnC 6ivoC 6ivpC 6ivqC 6ivrC 6ivwC 6jlfC 4wd8 C: citing same article (ref.)
Similar structure data	6jlf-d 4wd8-d 6ivq-d 6ivw-d 4wd7-d 6iv1-d 6ivn-d 6iv3-d 6ivp-d 6ivo-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

Deposited unit

A: Bestrophin homolog

B: Bestrophin homolog

C: Bestrophin homolog

D: Bestrophin homolog

E: Bestrophin homolog

hetero molecules

169 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	114.160, 160.109, 162.035
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Bestrophin homolog Mass: 33652.070 Da / Num. of mol.: 5 / Mutation: Y211A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae IS53 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: W1ELP7
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 36 / 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: 4.4 Å³/Da / Density % sol: 72.05 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.05M zinc acetate, 6% v/v ethylene glycol, 0.1M sodium cacodylate, pH 6.0, 6.6% w/v PEG 8000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 20, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 2.62→71.77 Å / Num. obs: 87896 / % possible obs: 97.2 % / Redundancy: 3.5 % / Net I/σ(I): 14.28
Reflection shell	Resolution: 2.62→2.71 Å

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Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Resolution: 2.62→71.773 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.37 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2626	1999	2.29 %
R_work	0.2239	-	-
obs	0.2249	87275	97.24 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.62→71.773 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10412	0	0	36	10448

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	10749
X-RAY DIFFRACTION	f_angle_d	0.87	14605
X-RAY DIFFRACTION	f_dihedral_angle_d	10.359	6410
X-RAY DIFFRACTION	f_chiral_restr	0.048	1748
X-RAY DIFFRACTION	f_plane_restr	0.006	1835

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 (%)
2.62-2.6855	0.3521	141	0.3329	6048	X-RAY DIFFRACTION	98
2.6855-2.7581	0.3131	145	0.3066	6119	X-RAY DIFFRACTION	99
2.7581-2.8393	0.3242	142	0.2854	6132	X-RAY DIFFRACTION	99
2.8393-2.931	0.3217	148	0.2777	6173	X-RAY DIFFRACTION	99
2.931-3.0357	0.3226	141	0.2654	6151	X-RAY DIFFRACTION	99
3.0357-3.1573	0.2771	147	0.2495	6145	X-RAY DIFFRACTION	99
3.1573-3.3009	0.2524	144	0.2401	6172	X-RAY DIFFRACTION	99
3.3009-3.475	0.2843	143	0.2307	6101	X-RAY DIFFRACTION	98
3.475-3.6927	0.2359	139	0.2202	6100	X-RAY DIFFRACTION	98
3.6927-3.9778	0.2635	143	0.2031	6027	X-RAY DIFFRACTION	96
3.9778-4.378	0.2509	143	0.2026	6034	X-RAY DIFFRACTION	96
4.378-5.0114	0.2352	141	0.1921	6034	X-RAY DIFFRACTION	96
5.0114-6.3133	0.3002	137	0.254	6019	X-RAY DIFFRACTION	94
6.3133-71.7996	0.2394	145	0.2092	6021	X-RAY DIFFRACTION	91

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	-0.0202	-0.1987	-0.0233	0.4323	0.0556	0.0208	-0.3883	0.5533	0.5014	-0.9221	-0.4248	1.5706	-0.1171	-1.9934	0.0081	0.9061	-0.4138	-0.1073	1.5847	-0.2552	1.2343	-51.4072	-3.1306	-28.9024
2	-0.351	-0.0809	-0.3302	-0.205	0.184	0.1865	-0.2259	-0.1084	-0.1277	0.1465	0.0576	-0.0396	0.5155	0.4665	0.0003	0.7082	-0.0235	0.0107	0.6802	-0.021	0.5411	-36.6339	14.7214	2.7454
3	1.0849	-0.3541	0.897	2.0389	-0.5426	0.5305	-0.1465	-0.0798	-0.2711	0.3524	0.2117	0.438	-0.0111	-0.2171	0.0001	0.5508	-0.0229	0.0736	0.6557	0.0645	0.6291	-45.8408	26.5871	19.8048
4	0.5649	0.0633	0.3951	0.3693	0.0147	0.2187	-0.3595	-0.1299	-0.0696	0.1771	0.1649	0.6632	-0.3084	-0.8698	0.0091	0.7384	-0.3092	0.0395	1.1566	-0.1791	0.7787	-45.1558	0.4862	-20.4902
5	0.4707	-0.0319	-0.1826	0.6208	0.0183	0.0671	0.0609	-0.2486	-0.4482	-0.3448	0.2297	0.3302	0.5982	0.0886	0.0062	0.9323	-0.0252	-0.068	0.7668	0.0222	0.875	-45.2709	11.8776	15.4987
6	0.1582	0.0685	-0.1473	0.3079	-0.362	0.1026	-0.7084	0.3254	0.7824	-0.9434	0.2538	-0.2911	-0.1967	0.0088	0.0073	1.4845	0.1051	-0.1545	1.0979	-0.0556	0.9426	-39.7909	15.8369	-42.8694
7	-0.1162	-0.1937	-0.0679	0.1361	-0.1008	0.0162	-0.4376	0.0436	-0.1131	0.3339	-0.0451	0.3725	0.7724	-0.4068	-0.0045	0.7145	-0.0305	0.1198	0.5976	-0.1309	0.5223	-34.9085	26.1915	-5.4926
8	1.2219	-0.0053	-0.4607	1.3152	-0.2238	0.4502	0.0626	-0.0074	0.5171	0.0504	-0.0621	0.2153	-0.3733	-0.1223	0.0023	0.5083	0.0487	0.0001	0.5536	-0.0317	0.6418	-37.5428	47.4537	7.6301
9	-0.011	-0.0099	-0.0138	0.0132	0.0293	0.0108	-0.0942	0.3698	-0.151	0.0625	-0.5613	-0.7028	-0.1384	0.3536	-0.0033	1.7335	-0.0667	0.5006	0.8438	0.1116	1.446	-27.798	34.541	-16.255
10	0.6454	-0.4706	-0.2583	0.3264	0.4319	0.873	-0.1062	0.5103	0.2993	-0.7082	0.3078	0.0932	-1.056	-0.2852	0.5925	1.0634	-0.0569	-0.082	0.9386	-0.057	0.7763	-38.5845	17.0644	-30.5739
11	1.4428	0.029	-0.2152	0.4876	-0.2943	0.163	-0.1183	0.6432	-0.2297	-0.4636	0.2517	0.6609	0.4918	-0.1273	0.0298	0.5326	0.0069	-0.0801	0.4655	0.0344	0.5173	-46.0894	35.9027	-0.4649
12	-0.005	-0.1218	0.2169	0.6873	-0.5503	0.6799	1.0166	0.168	0.8741	-0.9948	-0.3957	-0.3811	0.3445	-0.2209	0.2476	1.1798	-0.1519	0.4528	1.3724	-0.569	1.4735	-9.281	-10.2041	-29.2575
13	0.5537	0.067	-0.1699	0.4673	0.7575	0.1595	-0.2572	0.5467	-0.1057	0.3178	0.1943	0.0463	0.2062	0.5675	0.0186	0.452	-0.0735	-0	0.5336	-0.1252	0.532	-14.4537	17.4098	-2.2159
14	0.6497	0.7387	-0.5758	0.8189	-0.7245	1.2614	0.042	-0.2776	-0.2539	0.3358	-0.0158	-0.5021	0.064	0.5296	0.0002	0.6002	0.0519	-0.1839	0.7213	0.055	0.7697	-3.1199	24.0643	19.0848
15	0.7967	0.3213	-0.5264	2.8401	-0.2292	0.1957	0.121	-0.6426	0.2508	0.3289	0.3511	-0.7566	-0.2312	0.1167	0.2724	0.6225	-0.0876	0.1003	1.035	-0.3709	0.9577	-12.7322	-0.3558	-19.5591
16	0.1953	0.0177	-0.1204	0.2341	-0.3894	0.4221	-0.1411	0.0355	-0.0898	-0.9467	-0.2188	-0.8827	-0.326	0.8747	0.0004	0.6107	-0.0273	0.0142	0.6055	0.0158	0.71	-0.5776	23.8747	3.0686
17	0.0878	-0.1259	0.1935	0.0963	-0.1681	0.2635	0.3267	0.4815	-0.1378	0.0669	0.2915	0.6945	0.2355	0.8546	0.0217	0.9321	-0.2721	0.3938	1.3231	-0.3379	1.0689	-13.8199	10.8234	-42.6439
18	-0.8799	0.4214	-0.9772	-0.322	0.5149	0.1292	-0.2655	-0.014	0.0676	-0.6912	0.0223	0.5846	-0.7317	-0.095	0.0131	0.6022	0.021	-0.0498	0.4731	-0.0654	0.557	-21.3685	28.071	-8.3074
19	1.3449	0.6348	-0.0949	1.1012	-0.4207	0.325	-0.0155	-0.0469	0.2568	0.1095	-0.0142	-0.1202	-0.1364	0.242	0.0001	0.523	-0.0047	-0.0156	0.5186	0.0119	0.5952	-10.8546	45.9418	5.9666
20	0.7282	-0.6425	-0.0409	0.9235	-0.0169	0.0839	-0.6233	0.3097	0.083	-0.1691	0.3397	-0.2421	-0.4865	0.629	0.2896	0.9705	-0.2884	0.1371	0.8159	-0.091	0.8236	-17.3087	15.1952	-30.9842
21	0.3064	0.3034	0.1234	0.2556	-0.1642	0.3941	-0.073	0.6049	0.1668	-0.9448	0.2726	0.5928	-0.8429	-0.1773	-0.0004	0.8827	-0.0542	-0.0287	0.9226	0.0991	0.8006	-18.6096	42.4542	-9.3496
22	0.1448	-0.0305	-0.0628	0.0096	0.1054	0.1603	-0.561	0.2497	-0.3395	-0.6482	-0.0598	0.1221	0.8227	-0.44	-0.0006	1.6498	-0.1604	0.108	0.6701	0.0573	1.5324	-29.2387	-20.6437	-16.7255
23	0.3008	0.0757	-0.3605	0.4531	-0.0454	1.0983	-0.3599	0.5545	-0.291	0.0174	0.2369	-0.256	0.1146	0.6877	-0.2586	0.7051	-0.0712	0.0785	0.6557	-0.0617	0.5536	-26.9114	3.4822	-1.7552
24	0.4161	-0.2483	0.1151	0.4849	-0.5182	0.7069	0.2931	-0.7318	-0.3211	0.9182	-0.3971	-0.2276	0.3148	-0.0755	0.0016	1.0453	-0.1147	-0.0747	0.791	0.184	0.6658	-23.2957	6.7003	30.9945
25	0.2692	0.1991	-0.2023	0.0644	0.0115	0.0963	0.1245	-0.5266	0.1856	0.2482	-0.4551	0.2664	-0.0924	-0.4712	0.0004	0.6427	-0.0145	-0.0102	0.8006	0.0601	0.6029	-26.4255	19.2753	27.0763
26	0.1021	-0.1251	-0.0879	0.1556	0.0886	0.1093	0.1255	-0.4158	0.062	0.2474	0.1106	-0.3441	0.0426	0.0244	0.0102	1.5483	-0.1438	0.1718	1.7443	0.4786	1.2459	-38.5591	2.3076	1.2677
27	-0.0429	0.0047	-0.0402	0.0439	0.0231	0.0126	0.1601	-1.404	-0.9125	0.7603	0.0131	-0.1099	-0.1839	-0.2816	0.0002	1.0097	-0.26	0.2276	1.0725	0.0772	0.7781	-35.5495	-8.2204	-10.731
28	1.0329	0.5105	-0.4747	0.6911	-0.4388	0.3502	-0.5817	-0.8688	-1.8102	0.5263	-0.2519	0.0397	1.0684	0.7946	-0.1995	1.0915	-0.1085	0.1473	0.8364	-0.1887	1.2952	-25.933	-10.2286	-14.7734
29	0.0154	-0.0415	0.0092	0.0458	0.0032	0.0115	0.358	0.1354	-1.1805	0.4138	0.3808	-0.2631	0.8133	-0.5334	-0.0002	1.0546	-0.1746	0.1748	1.4571	-0.2595	1.0098	-23.806	-1.8014	9.6442
30	0.0747	-0.0043	0.0101	0.0338	-0.0546	0.0634	-0.1972	-0.8278	0.0193	0.5943	-0.1739	-1.6137	0.4598	0.9476	-0.0009	0.8727	0.1898	-0.0808	1.3017	0.0495	1.168	-11.9592	7.3671	24.0743

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 22:54 )	A	22 - 54
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 55:103 )	A	55 - 103
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 104:212 )	A	104 - 212
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 213:258 )	A	213 - 258
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 259:289 )	A	259 - 289
6	X-RAY DIFFRACTION	6	( CHAIN B AND RESID 22:54 )	B	22 - 54
7	X-RAY DIFFRACTION	7	( CHAIN B AND RESID 55:103 )	B	55 - 103
8	X-RAY DIFFRACTION	8	( CHAIN B AND RESID 104:202 )	B	104 - 202
9	X-RAY DIFFRACTION	9	( CHAIN B AND RESID 203:210 )	B	203 - 210
10	X-RAY DIFFRACTION	10	( CHAIN B AND RESID 211:259 )	B	211 - 259
11	X-RAY DIFFRACTION	11	( CHAIN B AND RESID 260:288 )	B	260 - 288
12	X-RAY DIFFRACTION	12	( CHAIN C AND RESID 24:53 )	C	24 - 53
13	X-RAY DIFFRACTION	13	( CHAIN C AND RESID 54:103 )	C	54 - 103
14	X-RAY DIFFRACTION	14	( CHAIN C AND RESID 104:204 )	C	104 - 204
15	X-RAY DIFFRACTION	15	( CHAIN C AND RESID 205:260 )	C	205 - 260
16	X-RAY DIFFRACTION	16	( CHAIN C AND RESID 261:288 )	C	261 - 288
17	X-RAY DIFFRACTION	17	( CHAIN D AND RESID 22:53 )	D	22 - 53
18	X-RAY DIFFRACTION	18	( CHAIN D AND RESID 54:103 )	D	54 - 103
19	X-RAY DIFFRACTION	19	( CHAIN D AND RESID 104:204 )	D	104 - 204
20	X-RAY DIFFRACTION	20	( CHAIN D AND RESID 205:255 )	D	205 - 255
21	X-RAY DIFFRACTION	21	( CHAIN D AND RESID 256:289 )	D	256 - 289
22	X-RAY DIFFRACTION	22	( CHAIN E AND RESID 25:43 )	E	25 - 43
23	X-RAY DIFFRACTION	23	( CHAIN E AND RESID 44:103 )	E	44 - 103
24	X-RAY DIFFRACTION	24	( CHAIN E AND RESID 104:155 )	E	104 - 155
25	X-RAY DIFFRACTION	25	( CHAIN E AND RESID 156:204 )	E	156 - 204
26	X-RAY DIFFRACTION	26	( CHAIN E AND RESID 205:211 )	E	205 - 211
27	X-RAY DIFFRACTION	27	( CHAIN E AND RESID 212:226 )	E	212 - 226
28	X-RAY DIFFRACTION	28	( CHAIN E AND RESID 227:261 )	E	227 - 261
29	X-RAY DIFFRACTION	29	( CHAIN E AND RESID 262:271 )	E	262 - 271
30	X-RAY DIFFRACTION	30	( CHAIN E AND RESID 272:289 )	E	272 - 289

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