PDB-4rdq: Calcium-activated chloride channel bestrophin-1, from chicken, in...

ID or keywords:

Entry

Database: PDB / ID: 4rdq

Title

Calcium-activated chloride channel bestrophin-1, from chicken, in complex with Fab antibody fragments, chloride and calcium

Components

(Fab antibody fragment, ...) x 2
Bestrophin-1Calcium-dependent chloride channel

Keywords

TRANSPORT PROTEIN /

transmembrane protein /

membrane protein /

ion channel /

calcium-activated chloride channel / CaCC /

anion channel /

membrane

Function / homology

Function and homology information

Stimuli-sensing channels /

chloride channel activity /

membrane /

metal ion binding
Similarity search - Function

Biological species

Gallus gallus (chicken)

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.85 Å

Authors

Dickson, V.K. / Pedi, L. / Long, S.B.

Citation

Journal: Nature / Year: 2014
Title: Structure and insights into the function of a Ca(2+)-activated Cl(-) channel.
Authors: Kane Dickson, V. / Pedi, L. / Long, S.B.

History

Deposition	Sep 19, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 22, 2014	Provider: repository / Type: Initial release
Revision 1.1	Oct 29, 2014	Group: Structure summary
Revision 1.2	Dec 24, 2014	Group: Database references
Revision 1.3	Jul 17, 2019	Group: Data collection / Refinement description / Category: software Item: _software.classification / _software.name / _software.version

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4rdq.cif.gz	1.5 MB	Display	PDBx/mmCIF format
PDB format	pdb4rdq.ent.gz	1.3 MB	Display	PDB format
PDBx/mmJSON format	4rdq.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/rd/4rdq ftp://data.pdbj.org/pub/pdb/validation_reports/rd/4rdq	HTTPS FTP

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Related structure data

Similar structure data	5t5n-d 8164 3g6j-d 4zyp-d 4913 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	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

A: Bestrophin-1

B: Bestrophin-1

C: Bestrophin-1

D: Bestrophin-1

E: Bestrophin-1

F: Fab antibody fragment, light chain

G: Fab antibody fragment, heavy chain

H: Fab antibody fragment, light chain

I: Fab antibody fragment, heavy chain

J: Fab antibody fragment, light chain

K: Fab antibody fragment, heavy chain

L: Fab antibody fragment, light chain

M: Fab antibody fragment, heavy chain

N: Fab antibody fragment, light chain

O: Fab antibody fragment, heavy chain

hetero molecules

479 kDa, 15 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)	98.540, 242.904, 172.757
Angle α, β, γ (deg.)	90.00, 93.68, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 5 molecules ABCDE

#1: Protein	Bestrophin-1 / Calcium-dependent chloride channel / Best1 Mass: 47614.344 Da / Num. of mol.: 5 / Fragment: UNP residues 2-405 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: Best1 bestrophin-1 / Production host: pichia pastoris (fungus) / References: UniProt: E1C3A0

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Antibody , 2 types, 10 molecules FHJLNGIKMO

#2: Antibody	Fab antibody fragment, light chain Mass: 23339.707 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Details: antibody secreted from hybridoma cells / Source: (natural) Mus musculus (house mouse)
#3: Antibody	Fab antibody fragment, heavy chain Mass: 23638.525 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Details: antibody secreted from hybridoma cells / Source: (natural) Mus musculus (house mouse)

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Non-polymers , 6 types, 45 molecules

#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Cl
#6: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#7: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#8: Chemical	ChemComp-C6N / 6-cyclohexyl-2-(4-cyclohexylbutyl)-2-({[4-O-(alpha-D-glucopyranosyl)-beta-D-glucopyranosyl]oxy}methyl)hexyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside Mass: 1001.157 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₄₇H₈₄O₂₂
#9: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 10 / 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: 4.36 Å³/Da / Density % sol: 71.8 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 5% PEG 4000, 75 mM KCl, 75 mM NaCl, 50 mM sodium acetate pH 4.0, 20% glycerol, 0.5 mM Cymal-6-NG (detergent), 10 mM Tris-HCl pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 19, 2013
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.1 Å / Relative weight: 1
Reflection	Resolution: 2.85→40 Å / Num. obs: 188162 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.8 % / B_iso Wilson estimate: 61.1 Å² / R_sym value: 0.113 / Net I/σ(I): 14.2
Reflection shell	Resolution: 2.85→2.95 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 1.1 / Num. unique all: 18682 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.9_1678)	refinement
SHARP		phasing
CNS	1.3	refinement
REFMAC		refinement
CBASS		data collection
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 2.85→39.891 Å / SU ML: 0.39 / σ(F): 0 / Phase error: 27.53 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2341	9438	5.03 %	RANDOM
R_work	0.2167	-	-	-
obs	0.2176	187788	99.74 %	-
all	-	188162	-	-

Solvent computation

Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.85→39.891 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	30715	0	400	10	31125

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	31985
X-RAY DIFFRACTION	f_angle_d	0.931	43700
X-RAY DIFFRACTION	f_dihedral_angle_d	15.41	11245
X-RAY DIFFRACTION	f_chiral_restr	0.038	4945
X-RAY DIFFRACTION	f_plane_restr	0.005	5505

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 (%)
2.85-2.8824	0.399	313	0.3779	5878	X-RAY DIFFRACTION	98
2.8824-2.9163	0.3581	334	0.3583	5890	X-RAY DIFFRACTION	100
2.9163-2.9518	0.3774	332	0.3492	5879	X-RAY DIFFRACTION	100
2.9518-2.9892	0.3547	314	0.3529	5945	X-RAY DIFFRACTION	99
2.9892-3.0285	0.3232	318	0.3358	5874	X-RAY DIFFRACTION	100
3.0285-3.07	0.3341	313	0.3266	5974	X-RAY DIFFRACTION	100
3.07-3.1138	0.3365	344	0.3263	5856	X-RAY DIFFRACTION	100
3.1138-3.1603	0.3333	320	0.3098	5897	X-RAY DIFFRACTION	99
3.1603-3.2096	0.3033	330	0.2942	5913	X-RAY DIFFRACTION	100
3.2096-3.2622	0.3066	314	0.2978	5984	X-RAY DIFFRACTION	100
3.2622-3.3185	0.299	312	0.2828	5895	X-RAY DIFFRACTION	100
3.3185-3.3788	0.2864	318	0.2713	5980	X-RAY DIFFRACTION	100
3.3788-3.4437	0.2547	263	0.2666	5972	X-RAY DIFFRACTION	100
3.4437-3.514	0.2477	340	0.2343	5969	X-RAY DIFFRACTION	100
3.514-3.5903	0.2356	330	0.2219	5874	X-RAY DIFFRACTION	100
3.5903-3.6738	0.2413	297	0.2153	5978	X-RAY DIFFRACTION	100
3.6738-3.7656	0.244	293	0.2053	5949	X-RAY DIFFRACTION	100
3.7656-3.8673	0.2347	321	0.2007	5972	X-RAY DIFFRACTION	100
3.8673-3.981	0.2049	339	0.195	5911	X-RAY DIFFRACTION	100
3.981-4.1094	0.2151	295	0.1866	6006	X-RAY DIFFRACTION	100
4.1094-4.2561	0.2082	339	0.1821	5910	X-RAY DIFFRACTION	100
4.2561-4.4263	0.1719	280	0.1733	5988	X-RAY DIFFRACTION	100
4.4263-4.6275	0.1978	307	0.1633	5972	X-RAY DIFFRACTION	100
4.6275-4.8711	0.216	302	0.182	5955	X-RAY DIFFRACTION	100
4.8711-5.1756	0.1974	323	0.186	5964	X-RAY DIFFRACTION	100
5.1756-5.5743	0.214	309	0.2013	5971	X-RAY DIFFRACTION	100
5.5743-6.1334	0.2391	290	0.209	5994	X-RAY DIFFRACTION	100
6.1334-7.0168	0.2395	292	0.2095	6015	X-RAY DIFFRACTION	100
7.0168-8.8246	0.1932	325	0.1685	5988	X-RAY DIFFRACTION	100
8.8246-39.8949	0.1923	331	0.1987	5997	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	0.5506	-0.0284	-0.0996	0.2055	-0.0405	0.4399	0.0232	-0.2196	0.2248	-0.0133	0.0297	-0.0977	-0.0649	0.0399	-0	0.4375	-0.0177	0.019	0.4455	-0.1711	0.5442	49.1308	84.7069	41.2728
2	0.3517	-0.0571	-0.0558	0.2984	0.0221	0.2064	0.0163	-0.3597	0.0604	0.068	0.0491	-0.0442	0.0344	0.0677	0	0.3919	0.0137	-0.0314	0.6268	-0.1731	0.4425	49.0637	72.9035	60.2726
3	0.2675	0.0133	-0.0389	0.2652	0.2239	0.3781	0.0107	-0.2638	-0.0957	0.0398	0.0111	-0.0526	0.0794	0.0502	0	0.3819	0.036	-0.032	0.5112	-0.046	0.376	48.9875	51.2244	54.9372
4	0.354	0.1098	0.0147	0.3584	-0.0892	0.3131	0.0131	-0.0035	-0.0218	-0.0582	0.0386	-0.0683	0.0223	0.0229	0	0.453	0.0255	0.0085	0.4279	-0.0805	0.465	48.9947	49.6212	32.643
5	0.5605	-0.0557	0.0614	0.4258	0.1296	0.2216	0.0147	-0.072	0.1808	-0.0614	0.0184	-0.0333	-0.0496	0.0465	-0	0.4253	-0.0061	0.0354	0.3961	-0.0849	0.4751	49.0724	70.307	24.1802
6	0.5052	-0.3326	-0.1281	1.4172	-0.0883	0.6569	-0.2552	0.1609	0.1763	0.0326	-0.1585	-0.1836	-0.2072	-0.1376	0	0.7309	-0.0391	-0.1397	0.6215	-0.122	0.8644	59.0613	117.296	27.1937
7	0.2282	-0.0059	-0.3014	0.6397	0.2615	0.9366	-0.0574	-0.3147	0.1237	-0.0209	0.2488	-0.1108	-0.1201	-0.0366	0.0075	0.6049	0.072	-0.0504	1.0033	-0.344	0.607	57.3942	97.1052	86.1151
8	0.2979	0.4568	0.1769	0.7469	0.039	0.7587	0.2395	-0.428	-0.2293	0.4775	-0.1144	-0.0909	0.4055	0.1957	0	1.0215	0.0483	-0.1228	1.1654	0.1917	0.7204	57.0296	33.7718	85.9242
9	0.6334	-0.1755	-0.2805	1.5802	0.0223	0.9165	-0.1672	-0.0598	-0.1841	-0.007	0.1393	-0.2181	0.0982	0.0124	0	0.6503	0.0169	0.0131	0.5011	-0.0714	0.6634	57.0228	14.8351	25.8713
10	0.8332	-0.7965	0.3858	1.1944	0.0085	1.1513	0.1544	0.1201	0.0369	-0.4296	-0.1163	-0.1668	0.0131	0.1765	0	0.832	-0.0034	0.1179	0.5462	0.0101	0.5792	57.6596	66.2308	-10.961
11	0.3253	-0.0095	-0.1986	0.591	-0.2549	0.1543	0.2854	-0.0067	-0.2215	0.0476	-0.0439	-0.1888	-0.2603	-0.0713	-0	1.5315	0.0492	-0.1999	0.8435	0.1064	1.1166	60.4914	152.1975	19.6285
12	0.6938	-0.4432	0.2653	0.4333	0.2683	0.8652	-0.0721	0.4001	-0.2066	0.3781	0.1671	0.0206	-0.3511	0.2547	-0	1.15	0.0146	0.0236	0.8586	-0.1696	0.7182	54.8384	116.3181	116.1061
13	0.0587	-0.0105	-0.0837	0.0246	-0.0664	0.1033	-0.6871	-0.4258	-0.7033	0.5875	0.1674	-0.0004	0.7691	-0.2048	-0	2.475	0.4111	0.2054	2.4587	0.8237	1.6242	53.9003	10.8746	113.5577
14	0.5798	0.1481	-0.541	0.6952	0.0667	0.5222	-0.0429	-0.0455	0.1034	-0.072	0.222	-0.1846	0.1559	-0.0686	-0	1.0206	0.0575	0.1634	0.7114	-0.1189	0.986	56.0367	-19.5485	16.3715
15	0.0404	0.1021	-0.103	0.0315	-0.0839	0.0723	-0.5096	1.1081	0.1057	-0.9789	0.3015	-0.1352	-0.0552	0.5063	0.0019	2.1115	-0.3009	0.1134	1.9608	0.1289	1.0226	56.3289	69.4245	-46.7202

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A'
2	X-RAY DIFFRACTION	2	chain 'B'
3	X-RAY DIFFRACTION	3	chain 'C'
4	X-RAY DIFFRACTION	4	chain 'D'
5	X-RAY DIFFRACTION	5	chain 'E'
6	X-RAY DIFFRACTION	6	(chain 'F' and resid 1 through 103) or (chain 'G' and resid 1 through 113)
7	X-RAY DIFFRACTION	7	(chain 'H' and resid 1 through 103) or (chain 'I' and resid 1 through 113)
8	X-RAY DIFFRACTION	8	(chain 'J' and resid 1 through 103) or (chain 'K' and resid 1 through 113)
9	X-RAY DIFFRACTION	9	(chain 'L' and resid 1 through 103) or (chain 'M' and resid 1 through 113)
10	X-RAY DIFFRACTION	10	(chain 'N' and resid 1 through 103) or (chain 'O' and resid 1 through 113)
11	X-RAY DIFFRACTION	11	(chain 'F' and resid 104 through 212) or (chain 'G' and resid 114 through 217)
12	X-RAY DIFFRACTION	12	(chain 'H' and resid 104 through 212) or (chain 'I' and resid 114 through 217)
13	X-RAY DIFFRACTION	13	(chain 'J' and resid 104 through 212) or (chain 'K' and resid 114 through 217)
14	X-RAY DIFFRACTION	14	(chain 'L' and resid 104 through 212) or (chain 'M' and resid 114 through 217)
15	X-RAY DIFFRACTION	15	(chain 'N' and resid 104 through 212) or (chain 'O' and resid 114 through 217)

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