PDB-4wd7: Crystal structure of a bacterial Bestrophin homolog from Klebsiel...

ID or keywords:

Entry

Database: PDB / ID: 4wd7

Title

Crystal structure of a bacterial Bestrophin homolog from Klebsiella pneumoniae by Zn-SAD phasing

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: 2.9 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.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.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	4wd7.cif.gz	542.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4wd7.ent.gz	453.5 KB	Display	PDB format
PDBx/mmJSON format	4wd7.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4wd7_validation.pdf.gz	469 KB	Display	wwPDB validaton report
Full document	4wd7_full_validation.pdf.gz	484.5 KB	Display
Data in XML	4wd7_validation.xml.gz	44.9 KB	Display
Data in CIF	4wd7_validation.cif.gz	60.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wd/4wd7 ftp://data.pdbj.org/pub/pdb/validation_reports/wd/4wd7	HTTPS FTP

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Related structure data

Related structure data	4wd8C C: citing same article (ref.)
Similar structure data	6ivq-d 4wd8-d 6ivp-d 6ivw-d 6iv3-d 6iv1-d 6ivo-d 6jlf-d 6ivn-d 5x87-d 6iv2-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

172 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)	114.124, 160.587, 161.745
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: 34299.812 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

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 4.32 Å³/Da / Density % sol: 71.54 %
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: NSLS / Beamline: X4A / Wavelength: 1.2821 Å
Detector	Type: ADSC QUANTUM 4r / Detector: CCD / Date: Feb 26, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.2821 Å / Relative weight: 1
Reflection	Resolution: 2.9→40 Å / Num. obs: 66573 / % possible obs: 100 % / Redundancy: 29.4 % / Net I/σ(I): 29.1

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Processing

Software

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

Refinement

Method to determine structure:

SAD / Resolution: 2.9→39.189 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.22 / Phase error: 25.81 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2528	6288	4.94 %
R_work	0.2392	-	-
obs	0.2399	127171	99.95 %

Solvent computation

Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.9→39.189 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10636	0	15	0	10651

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	10902
X-RAY DIFFRACTION	f_angle_d	0.881	14806
X-RAY DIFFRACTION	f_dihedral_angle_d	10.69	3931
X-RAY DIFFRACTION	f_chiral_restr	0.057	1761
X-RAY DIFFRACTION	f_plane_restr	0.004	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 (%)
2.9-2.933	0.3462	239	0.3487	4019	X-RAY DIFFRACTION	100
2.933-2.9674	0.3155	166	0.3324	4028	X-RAY DIFFRACTION	100
2.9674-3.0036	0.3092	209	0.324	4075	X-RAY DIFFRACTION	100
3.0036-3.0416	0.3312	231	0.3243	4017	X-RAY DIFFRACTION	100
3.0416-3.0816	0.3036	227	0.3082	3995	X-RAY DIFFRACTION	100
3.0816-3.1238	0.2882	174	0.304	4029	X-RAY DIFFRACTION	100
3.1238-3.1684	0.3129	229	0.3011	4047	X-RAY DIFFRACTION	100
3.1684-3.2157	0.3002	168	0.2978	4055	X-RAY DIFFRACTION	100
3.2157-3.2659	0.2957	208	0.3029	4051	X-RAY DIFFRACTION	100
3.2659-3.3195	0.3046	207	0.2839	3973	X-RAY DIFFRACTION	100
3.3195-3.3767	0.2987	216	0.2692	4048	X-RAY DIFFRACTION	100
3.3767-3.438	0.2629	221	0.2693	4059	X-RAY DIFFRACTION	100
3.438-3.5041	0.2572	228	0.2554	4010	X-RAY DIFFRACTION	100
3.5041-3.5756	0.248	229	0.2478	4014	X-RAY DIFFRACTION	100
3.5756-3.6533	0.2841	224	0.2511	4009	X-RAY DIFFRACTION	100
3.6533-3.7382	0.2672	218	0.2454	4019	X-RAY DIFFRACTION	100
3.7382-3.8316	0.2744	188	0.2354	4036	X-RAY DIFFRACTION	100
3.8316-3.9351	0.2341	209	0.2279	4073	X-RAY DIFFRACTION	100
3.9351-4.0508	0.2592	183	0.2258	4026	X-RAY DIFFRACTION	100
4.0508-4.1814	0.2729	225	0.2329	4023	X-RAY DIFFRACTION	100
4.1814-4.3307	0.2332	179	0.22	4039	X-RAY DIFFRACTION	100
4.3307-4.5038	0.2214	218	0.2141	4034	X-RAY DIFFRACTION	100
4.5038-4.7085	0.2533	198	0.2145	4023	X-RAY DIFFRACTION	100
4.7085-4.9563	0.2273	194	0.2158	4080	X-RAY DIFFRACTION	100
4.9563-5.2661	0.2582	212	0.2294	4000	X-RAY DIFFRACTION	100
5.2661-5.6716	0.2783	202	0.2465	4052	X-RAY DIFFRACTION	100
5.6716-6.2403	0.2616	232	0.2583	4000	X-RAY DIFFRACTION	100
6.2403-7.1386	0.2934	259	0.2351	4005	X-RAY DIFFRACTION	100
7.1386-8.976	0.2227	202	0.191	4039	X-RAY DIFFRACTION	100
8.976-39.1926	0.1708	193	0.2208	4005	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	2.9373	1.0306	-1.2495	1.6002	-1.5455	1.2702	-0.2036	-0.787	0.1997	0.6366	0.1693	-0.3608	0.4774	0.791	-0.0014	1.1044	0.2741	-0.1856	1.0665	-0.2004	0.7017	-17.832	-14.5818	32.9931
2	3.2032	0.335	1.3536	3.9555	0.7501	3.5476	0.0354	-0.1955	-0.4687	0.1726	0.0625	-0.1954	0.5157	-0.047	0.0005	0.5589	-0.0092	-0.0163	0.6318	0.0425	0.7839	-14.1344	-44.5079	-2.4207
3	1.1974	-0.6035	0.3998	2.1581	-0.2933	0.6776	-0.0135	-0.1757	0.7653	-0.2671	0.2671	-0.7336	-0.9668	0.6735	0.001	0.9824	-0.037	-0.1193	0.9295	-0.3212	1.1252	-14.0611	2.5881	22.9234
4	2.5413	-1.2695	0.4922	4.4432	0.0756	3.6849	-0.2086	0.0917	0.29	-0.6004	0.1381	-1.1177	-0.1754	0.4582	0.0003	0.5791	-0.0446	0.2045	0.6733	0.0474	0.9467	-3.7889	-24.0997	-13.3888
5	2.6815	0.5062	-0.217	3.2495	-2.5301	2.1366	-0.0792	-0.0603	0.4085	0.2725	-0.1927	1.1063	0.4663	-1.1245	0.0005	0.846	0.2333	0.0547	1.1104	-0.243	1.0414	-45.9173	-2.4931	21.8732
6	2.1568	0.0939	-0.5553	3.8652	0.9575	3.4932	-0.0432	0.1716	0.3233	-0.7212	-0.0656	0.6211	-0.235	-0.3638	-0.0005	0.7881	-0.0529	-0.1264	0.7277	0.0854	0.6929	-43.5513	-22.3665	-19.9542
7	2.5914	-1.251	0.6946	2.7105	-1.2364	1.3357	-0.0862	0.2294	0.9363	-0.3079	-0.0698	0.1131	-1.3092	-0.3995	-0.0052	1.1803	0.161	-0.041	0.7369	-0.1378	1.0686	-31.3656	9.7538	15.7808
8	3.8518	-0.789	-0.1952	5.15	0.2759	3.6016	-0.1939	0.3282	0.2028	-0.8379	-0.0271	-0.36	-0.639	0.1826	-0.0003	0.8573	-0.0893	0.0045	0.7901	0.1498	0.6325	-21.5888	-11.1826	-24.4569
9	2.4643	0.9423	-0.9091	2.0617	-0.7146	1.7526	-0.0537	-0.3086	-0.072	0.8871	-0.0697	0.3943	0.5275	-0.3909	-0.0037	1.1388	-0.0109	0.1261	0.9854	-0.2203	0.8012	-37.3844	-17.4766	32.7876
10	4.3644	0.7585	-0.1892	4.9817	0.4717	3.9072	-0.081	-0.1122	-0.1653	-0.0273	-0.0519	0.4055	0.3118	-0.2156	0.0006	0.4718	-0.0345	-0.0457	0.6132	0.0072	0.6669	-39.4146	-42.7899	-6.1837

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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