PDB-4wd8: Crystal structure of a bacterial Bestrophin homolog from Klebsiel...

ID or keywords:

Entry

Database: PDB / ID: 4wd8

Title

Crystal structure of a bacterial Bestrophin homolog from Klebsiella pneumoniae

Components

Bestrophin domain protein

Keywords

MEMBRANE PROTEIN / Calcium-activated chloride channel / Macular degeneration / Single-wavelength anomalous diffraction (SAD) / Sodium channel / pentamer / Structural Genomics / PSI-Biology / New York Consortium on Membrane Protein Structure / NYCOMPS

Function / homology

:

Function and homology information

Biological species

Klebsiella pneumoniae UHKPC96 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.3 Å

Authors

Yang, T. / Liu, Q. / Hendrickson, W.A. / New York Consortium on Membrane Protein Structure (NYCOMPS)

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM095315	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM107462	United States

Citation

Journal: Science / Year: 2014
Title: Structure and selectivity in bestrophin ion channels.
Authors: Yang, T. / Liu, Q. / Kloss, B. / Bruni, R. / Kalathur, R.C. / Guo, Y. / Kloppmann, E. / Rost, B. / Colecraft, H.M. / Hendrickson, W.A.

History

Deposition	Sep 8, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 1, 2014	Provider: repository / Type: Initial release
Revision 1.1	Oct 29, 2014	Group: Database references
Revision 1.2	Sep 6, 2017	Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy / Structure summary Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.3	Dec 25, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Dec 27, 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_struct_conn_angle / refine_hist / 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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.ptnr3_symmetry / _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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4wd8.cif.gz	549.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4wd8.ent.gz	454.9 KB	Display	PDB format
PDBx/mmJSON format	4wd8.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4wd8_validation.pdf.gz	474.2 KB	Display	wwPDB validaton report
Full document	4wd8_full_validation.pdf.gz	491.3 KB	Display
Data in XML	4wd8_validation.xml.gz	49.6 KB	Display
Data in CIF	4wd8_validation.cif.gz	69.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wd/4wd8 ftp://data.pdbj.org/pub/pdb/validation_reports/wd/4wd8	HTTPS FTP

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Related structure data

Related structure data	4wd7C C: citing same article (ref.)
Similar structure data	6iv3-d 6ivq-d 4wd7-d 6ivp-d 6ivw-d 6jlf-d 6ivn-d 6iv2-d 6ivm-d 6ivl-d 6ivo-d 6iv1-d 6ivj-d 6ivr-d 6ivk-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Bestrophin domain protein

B: Bestrophin domain protein

C: Bestrophin domain protein

D: Bestrophin domain protein

E: Bestrophin domain protein

hetero molecules

170 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)	114.079, 160.034, 161.881
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Bestrophin domain protein Mass: 33831.242 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae UHKPC96 (bacteria) Gene: H215_4284 / Production host: Escherichia coli (E. coli) / References: UniProt: S7AS11
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Zn
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 365 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 4.37 Å³/Da / Density % sol: 71.84 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.05 M zinc acetate, 6% v/v ethylene glycol, 0.1 M sodium cacodylate, pH 6.0, 6.6 % w/v PEG 8000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 25, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 2.3→40 Å / Num. obs: 131752 / % possible obs: 99.9 % / Redundancy: 12.4 % / Net I/σ(I): 11.8

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Processing

Software

Name: PHENIX / Version: (phenix.refine: 1.8.1_1168) / Classification: refinement

Refinement

Method to determine structure:

SAD / Resolution: 2.3→38.961 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0.93 / Phase error: 21.69 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2145	12418	4.89 %
R_work	0.1962	-	-
obs	0.1971	254129	99.91 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.3→38.961 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10636	0	15	365	11016

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	10924
X-RAY DIFFRACTION	f_angle_d	0.955	14806
X-RAY DIFFRACTION	f_dihedral_angle_d	11.076	3931
X-RAY DIFFRACTION	f_chiral_restr	0.06	1761
X-RAY DIFFRACTION	f_plane_restr	0.005	1861

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 (%)
2.3-2.3261	0.3312	357	0.3089	8176	X-RAY DIFFRACTION	100
2.3261-2.3535	0.286	410	0.3029	8037	X-RAY DIFFRACTION	100
2.3535-2.3822	0.3031	406	0.2883	8137	X-RAY DIFFRACTION	100
2.3822-2.4123	0.319	401	0.2933	7998	X-RAY DIFFRACTION	100
2.4123-2.4441	0.3231	450	0.2847	8075	X-RAY DIFFRACTION	100
2.4441-2.4776	0.2909	476	0.2701	7972	X-RAY DIFFRACTION	100
2.4776-2.5129	0.2955	425	0.2565	7997	X-RAY DIFFRACTION	100
2.5129-2.5505	0.2881	425	0.2462	8044	X-RAY DIFFRACTION	100
2.5505-2.5903	0.2588	461	0.2405	8093	X-RAY DIFFRACTION	100
2.5903-2.6328	0.2498	361	0.2363	8104	X-RAY DIFFRACTION	100
2.6328-2.6781	0.2342	414	0.2297	8058	X-RAY DIFFRACTION	100
2.6781-2.7268	0.2316	314	0.2198	8133	X-RAY DIFFRACTION	100
2.7268-2.7793	0.2235	449	0.2088	8054	X-RAY DIFFRACTION	100
2.7793-2.836	0.2443	389	0.2094	8082	X-RAY DIFFRACTION	100
2.836-2.8976	0.2246	397	0.2006	8071	X-RAY DIFFRACTION	100
2.8976-2.965	0.2017	410	0.1991	8116	X-RAY DIFFRACTION	100
2.965-3.0391	0.2196	443	0.1904	8003	X-RAY DIFFRACTION	100
3.0391-3.1213	0.1957	401	0.1868	8075	X-RAY DIFFRACTION	100
3.1213-3.2131	0.2332	394	0.1997	8073	X-RAY DIFFRACTION	100
3.2131-3.3167	0.2169	415	0.1976	8064	X-RAY DIFFRACTION	100
3.3167-3.4352	0.2105	441	0.1886	8040	X-RAY DIFFRACTION	100
3.4352-3.5726	0.1979	454	0.1782	8062	X-RAY DIFFRACTION	100
3.5726-3.7351	0.1961	441	0.172	8010	X-RAY DIFFRACTION	100
3.7351-3.9319	0.1777	404	0.1651	8095	X-RAY DIFFRACTION	100
3.9319-4.1779	0.2051	401	0.1689	8051	X-RAY DIFFRACTION	100
4.1779-4.5001	0.1634	391	0.1606	8055	X-RAY DIFFRACTION	100
4.5001-4.9522	0.1968	396	0.1694	8127	X-RAY DIFFRACTION	100
4.9522-5.6669	0.2103	416	0.1925	8051	X-RAY DIFFRACTION	100
5.6669-7.1325	0.2609	489	0.2211	7983	X-RAY DIFFRACTION	100
7.1325-38.9667	0.1686	387	0.184	7875	X-RAY DIFFRACTION	97

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	1.3553	1.0101	-1.1524	0.8163	-0.3446	4.677	-0.3496	-0.7505	0.2106	0.7997	0.3751	-0.4177	0.5483	0.9198	-0.1035	0.7706	0.3829	-0.2427	0.7183	-0.2542	0.4133	-17.8184	-14.6089	33.0096
2	2.5384	-0.4225	1.2318	1.6105	-0.3862	3.5451	0.021	-0.0503	-0.2945	-0.0435	0.0318	0.1518	0.3535	-0.086	-0.0361	0.113	-0.0007	0.0052	0.1564	0.0072	0.2598	-14.1528	-44.5482	-2.5041
3	0.8373	0.5856	0.482	3.1787	2.0176	2.5667	-0.0318	-0.3573	0.8267	0.0615	0.3077	-1.0244	-0.8536	0.5685	-0.2965	0.6324	0.0057	-0.2618	0.479	-0.3755	0.7584	-14.0338	2.5703	22.9661
4	2.2263	-1.0233	0.1281	3.337	0.7022	3.0906	-0.0344	0.2555	0.442	-0.2842	0.0921	-0.9035	-0.225	0.5323	-0.0215	0.152	-0.0311	0.0756	0.2963	0.0731	0.4213	-3.8248	-24.0979	-13.4518
5	3.7091	-1.1152	-2.5807	3.6093	0.7811	4.9913	-0.246	0.0797	0.2199	0.3852	-0.2733	0.7705	0.0715	-1.3989	0.4009	0.4385	0.2336	-0.0468	0.6746	-0.2389	0.5241	-45.8873	-2.4709	21.9135
6	2.5889	-0.4114	-0.4533	2.3345	0.6082	3.2649	0.0581	0.2546	0.2896	-0.2984	-0.0106	0.2405	-0.303	-0.2356	-0.04	0.2059	-0.029	-0.0367	0.2089	0.0857	0.2207	-43.6094	-22.3347	-19.9198
7	2.0572	-0.8327	-0.6974	4.9138	1.4244	1.8777	-0.0365	0.0397	0.7317	-0.4219	-0.0635	-0.0585	-1.2421	-0.6021	0.062	0.7717	0.2051	-0.1248	0.3501	-0.1411	0.547	-31.3309	9.7726	15.8191
8	2.3453	-0.4806	-0.2927	3.3735	0.4755	2.8289	-0.0372	0.4035	0.321	-0.5184	-0.0832	-0.2917	-0.6154	0.11	0.0893	0.3484	-0.0306	-0.0156	0.3527	0.1719	0.2775	-21.6287	-11.1403	-24.4761
9	3.4307	0.8724	-0.7471	1.371	0.8932	5.4967	-0.1917	-0.632	-0.0459	1.0727	0.0437	0.2554	0.8475	-0.2297	0.1265	0.7356	0.1351	0.0326	0.4447	-0.0901	0.3264	-37.3795	-17.4901	32.8362
10	3.5952	0.0802	-0.2144	2.1887	0.1533	2.6815	-0.0573	-0.0951	-0.3176	0.0676	-0.0132	0.145	0.2793	-0.1315	0.0592	0.1254	-0.0275	-0.0215	0.1498	0.0106	0.248	-39.482	-42.7694	-6.2059

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain A and (resseq 22:74 or resseq 206:260)
2	X-RAY DIFFRACTION	2	chain A and (resseq 75:205 or resseq 261:289)
3	X-RAY DIFFRACTION	3	chain B and (resseq 22:74 or resseq 206:260)
4	X-RAY DIFFRACTION	4	chain B and (resseq 75:205 or resseq 261:285)
5	X-RAY DIFFRACTION	5	chain C and (resseq 22:74 or resseq 206:260)
6	X-RAY DIFFRACTION	6	chain C and (resseq 75:205 or resseq 261:291)
7	X-RAY DIFFRACTION	7	chain D and (resseq 22:74 or resseq 206:260)
8	X-RAY DIFFRACTION	8	chain D and (resseq 75:205 or resseq 261:289)
9	X-RAY DIFFRACTION	9	chain E and (resseq 24:74 or resseq 206:260)
10	X-RAY DIFFRACTION	10	chain E and (resseq 75:205 or resseq 261:293)

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