PDB-5kn3: Recombinant bovine skeletal calsequestrin, low-Ca2+ form

ID or keywords:

Entry

Database: PDB / ID: 5kn3

Title

Recombinant bovine skeletal calsequestrin, low-Ca2+ form

Components

Calsequestrin

Keywords

METAL BINDING PROTEIN / calsequestrin / polymer / calcium

Function / homology

Function and homology information

Stimuli-sensing channels / regulation of store-operated calcium entry / Ion homeostasis / sarcoplasmic reticulum lumen / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / endoplasmic reticulum organization / sarcomere organization / protein polymerization / sarcoplasmic reticulum membrane / positive regulation of release of sequestered calcium ion into cytosol ...
Similarity search - Function

Biological species

Bos taurus (cattle)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.849 Å

Authors

Lewis, K.M. / Byrd, S. / Kang, C.

Funding support

United States, 2items

Citation

Journal: Int J Mol Sci / Year: 2016
Title: Characterization of Post-Translational Modifications to Calsequestrins of Cardiac and Skeletal Muscle.
Authors: Lewis, K.M. / Munske, G.R. / Byrd, S.S. / Kang, J. / Cho, H.J. / Rios, E. / Kang, C.

History

Deposition	Jun 27, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 5, 2016	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 2017	Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Dec 25, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Sep 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_initial_refinement_model / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5kn3.cif.gz	227 KB	Display	PDBx/mmCIF format
PDB format	pdb5kn3.ent.gz	184.3 KB	Display	PDB format
PDBx/mmJSON format	5kn3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5kn3_validation.pdf.gz	440.3 KB	Display	wwPDB validaton report
Full document	5kn3_full_validation.pdf.gz	441.7 KB	Display
Data in XML	5kn3_validation.xml.gz	17.9 KB	Display
Data in CIF	5kn3_validation.cif.gz	26.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kn/5kn3 ftp://data.pdbj.org/pub/pdb/validation_reports/kn/5kn3	HTTPS FTP

-
Related structure data

Related structure data	5kn0C 5kn1C 5kn2C 3trpS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3us3-1 5kn0-2 5crd-2 5kn0-1 3trp-2 3v1w-2 1sji-d 3szo-d 3trq-2 2z7e-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Calsequestrin

hetero molecules

42.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Calsequestrin

hetero molecules

A: Calsequestrin

hetero molecules

defined by author&software
84.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	59.393, 146.060, 110.340
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

#1: Protein	Calsequestrin Mass: 41554.277 Da / Num. of mol.: 1 / Fragment: UNP residues 35-395 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: casq1, CASQ1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q05JF3
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Chemical	ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#4: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 336 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.88 Å³/Da / Density % sol: 57.28 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1 M HEPES, 27.5 % 2-methyl-2,4-pentanediol, 0.2 M NaCl

-
Data collection

Diffraction	Mean temperature: 80 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 17, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.849→49.237 Å / Num. obs: 41309 / % possible obs: 100 % / Redundancy: 7.1 % / R_merge(I) obs: 0.0698 / Net I/σ(I): 13.4
Reflection shell	Resolution: 1.849→1.915 Å / Redundancy: 6.6 % / R_merge(I) obs: 0.8201 / Mean I/σ(I) obs: 2.72 / Num. measured obs: 3984 / % possible all: 97

-
Processing

Software

Name	Version	Classification
PHENIX	1.10_2155	refinement
HKL-2000	v712	data reduction
HKL-2000	v712	data scaling
PHENIX	1.10_2155	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3TRP

3trp

Resolution: 1.849→49.237 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.09

	R_factor	Num. reflection	% reflection
R_free	0.2106	1998	4.84 %
R_work	0.1833	-	-
obs	0.1847	41248	99.51 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å

Refinement step

Cycle: LAST / Resolution: 1.849→49.237 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2810	0	37	336	3183

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	2922
X-RAY DIFFRACTION	f_angle_d	0.568	3976
X-RAY DIFFRACTION	f_dihedral_angle_d	16.728	1755
X-RAY DIFFRACTION	f_chiral_restr	0.045	428
X-RAY DIFFRACTION	f_plane_restr	0.003	527

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 (%)
1.8489-1.8951	0.3275	134	0.296	2631	X-RAY DIFFRACTION	95
1.8951-1.9464	0.3062	141	0.2778	2785	X-RAY DIFFRACTION	100
1.9464-2.0037	0.295	142	0.2445	2775	X-RAY DIFFRACTION	100
2.0037-2.0683	0.2583	142	0.2285	2792	X-RAY DIFFRACTION	100
2.0683-2.1423	0.2291	142	0.2174	2780	X-RAY DIFFRACTION	100
2.1423-2.228	0.2336	141	0.2085	2777	X-RAY DIFFRACTION	100
2.228-2.3294	0.239	142	0.2049	2804	X-RAY DIFFRACTION	100
2.3294-2.4522	0.2605	142	0.196	2805	X-RAY DIFFRACTION	100
2.4522-2.6059	0.2365	143	0.2039	2799	X-RAY DIFFRACTION	100
2.6059-2.8071	0.2226	144	0.2021	2816	X-RAY DIFFRACTION	100
2.8071-3.0895	0.2249	142	0.1994	2806	X-RAY DIFFRACTION	100
3.0895-3.5365	0.2069	145	0.1777	2837	X-RAY DIFFRACTION	100
3.5365-4.4551	0.1619	146	0.1394	2867	X-RAY DIFFRACTION	100
4.4551-49.2543	0.1835	152	0.1603	2976	X-RAY DIFFRACTION	100

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	0.0013	-0.009	0.0008	0.0146	0.0046	0.0127	-0.1383	0.4015	-0.1072	-0.0116	-0.2372	0.0682	0.2848	-0.1051	0.0003	0.5096	0.0143	0.0041	0.4916	0.0333	0.3327	9.4073	2.994	-42.5774
2	1.0305	0.3292	0.3461	0.1991	-0.0781	0.559	-0.3287	-0.0479	-0.4125	0.1165	0.192	0.0861	0.286	0.2021	-0.243	0.634	0.1994	0.1457	0.3251	0.0646	0.3436	14.0321	-10.0217	-22.7564
3	0.0619	0.0457	0.0177	0.0372	-0.0067	0.0227	-0.2376	-0.124	0.4577	0.1655	0.5986	-0.6363	0.487	0.8372	0.0066	0.549	0.2274	-0.0355	0.6552	0.0231	0.5496	22.4974	-4.9466	-14.9798
4	0.4324	-0.3513	-0.0819	0.4222	0.1384	0.0812	-0.1496	-0.1731	0.0696	0.2373	0.2214	-0.0683	0.3092	-0.0246	-0.0403	0.5146	0.0991	0.098	0.3056	0.1384	0.3218	6.3209	-7.6823	-13.2039
5	0.9295	0.2955	0.4802	0.9901	-0.3055	0.9731	-0.2962	-0.1224	-0.3339	-0.1297	0.0691	-0.0125	0.5745	0.2059	0.0112	0.4621	0.0672	0.1248	0.2201	0.0546	0.3272	6.0878	-6.1189	-21.9451
6	0.1316	-0.0422	-0.2117	0.0344	0.0565	0.3504	-0.109	-0.2762	-0.062	-0.0801	0.1692	0.0404	0.1347	-0.0535	-0.1411	0.8988	0.362	0.2377	0.583	0.5023	0.3431	12.0886	-13.3514	-7.8623
7	0.5139	-0.4123	0.0394	0.4355	-0.0801	0.1758	-0.4673	-0.5037	-0.1684	0.444	0.1582	-0.0993	0.2383	0.1496	-0.1547	0.5208	0.2239	0.011	0.4428	0.0744	0.3033	11.7836	-0.8634	-7.6438
8	0.0375	-0.0194	0.0519	0.0549	-0.0013	0.076	-0.1069	-0.0782	0.2946	0.123	0.1151	0.0388	0.0916	0.0872	0.0001	0.3246	0.0514	0.0205	0.2892	-0.0069	0.2797	7.4677	6.9402	-18.5591
9	-0.001	0.0113	-0.0013	0.0255	0.0071	0.0145	-0.0834	0.0248	-0.0381	-0.3237	-0.0604	0.0781	-0.1803	0.1752	-0.0001	0.2981	0.013	-0.0071	0.4855	-0.0671	0.4039	21.0921	21.4447	-16.0422
10	0.0288	-0.035	0.0239	0.0656	0.0067	0.0686	0.0017	0.7032	0.4022	-0.0516	0.0228	0.0546	-0.0655	0.1993	0.0001	0.2722	-0.0495	-0.0336	0.4469	0.0735	0.3659	12.1034	29.4152	-18.618
11	0.3941	0.2774	0.2406	0.6499	0.3718	0.7068	-0.0124	0.0542	0.0495	-0.0086	0.0515	-0.0456	-0.0545	0.2355	0	0.2265	-0.0102	-0.0106	0.301	-0.0218	0.304	19.624	25.8086	-7.4704
12	0.0317	0.0328	-0.0165	0.0294	-0.0306	0.0309	-0.3048	-0.073	0.4903	-0.1032	0.0939	0.0706	-0.3417	-0.0689	0	0.3311	0.0238	-0.0632	0.3285	-0.061	0.4656	5.0494	31.3402	-7.1638
13	0.1861	-0.0512	-0.0195	0.0336	0.0145	0.1637	0.0169	-0.6459	-0.2275	0.2268	-0.0005	0.1798	0.039	-0.1289	0.0013	0.2635	-0.0071	0.0064	0.3161	-0.0046	0.2679	14.9859	22.4974	2.4212
14	0.0496	0.0421	0.0263	0.0588	-0.0034	0.0245	-0.0374	-0.2415	0.2676	-0.0677	0.0407	-0.215	0.0401	0.3291	-0	0.2174	0.0088	-0.0133	0.2941	-0.0664	0.3097	-1.1547	19.9171	-7.902
15	0.1318	0.0512	0.0167	0.1261	-0.0567	0.0291	-0.0084	-0.031	0.0549	0.1313	0.15	0.029	0.2801	0.2007	-0.0001	0.3232	0.0277	0.0379	0.2639	-0.0061	0.3054	-2.96	11.4713	-8.5804
16	0.219	0.0564	-0.0202	0.2184	0.1341	0.094	-0.0751	0.1228	0.0903	-0.0426	0.0038	0.1081	-0.2999	-0.1325	-0	0.2782	0.0211	-0.0073	0.2476	0.016	0.2218	-9.9384	23.8502	-17.8746
17	0.1807	0.0681	0.0761	0.0305	-0.0223	0.0862	0.0063	-0.4012	0.528	-0.0533	-0.2683	0.1051	0.1577	-0.4282	-0.0171	0.3158	0.0186	0.0034	0.3164	-0.0804	0.3073	-5.7638	28.9546	-6.1466
18	0.4654	0.1658	0.0874	0.3708	0.3064	0.1813	-0.1334	0.0355	-0.0194	-0.0552	-0.0322	0.0949	0.044	-0.1751	-0	0.2585	-0.0175	0.0126	0.2722	-0.0445	0.2632	-14.095	14.8855	-16.3476
19	0.0298	0.0052	0.0232	0.0009	-0.0101	0.0102	-0.1907	-0.0272	0.0745	-0.2737	0.0433	0.0796	-0.1088	-0.2319	-0.0001	0.4443	0.0644	-0.1212	0.5436	0.0129	0.5308	-22.3079	30.2214	-20.4103
20	0.0678	-0.0497	-0.0497	0.0473	0.0255	0.0533	0.0235	-0.1024	0.4968	0.3306	0.0742	0.2711	-0.2883	-0.413	0.0001	0.2496	0.0174	-0.0051	0.364	-0.1248	0.4722	-17.9806	28.5826	-5.8537

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 3:8)
2	X-RAY DIFFRACTION	2	(chain A and resid 9:22)
3	X-RAY DIFFRACTION	3	(chain A and resid 23:31)
4	X-RAY DIFFRACTION	4	(chain A and resid 32:42)
5	X-RAY DIFFRACTION	5	(chain A and resid 43:78)
6	X-RAY DIFFRACTION	6	(chain A and resid 79:84)
7	X-RAY DIFFRACTION	7	(chain A and resid 85:104)
8	X-RAY DIFFRACTION	8	(chain A and resid 105:123)
9	X-RAY DIFFRACTION	9	(chain A and resid 124:131)
10	X-RAY DIFFRACTION	10	(chain A and resid 132:145)
11	X-RAY DIFFRACTION	11	(chain A and resid 146:199)
12	X-RAY DIFFRACTION	12	(chain A and resid 200:207)
13	X-RAY DIFFRACTION	13	(chain A and resid 208:225)
14	X-RAY DIFFRACTION	14	(chain A and resid 226:233)
15	X-RAY DIFFRACTION	15	(chain A and resid 234:247)
16	X-RAY DIFFRACTION	16	(chain A and resid 248:265)
17	X-RAY DIFFRACTION	17	(chain A and resid 266:283)
18	X-RAY DIFFRACTION	18	(chain A and resid 284:325)
19	X-RAY DIFFRACTION	19	(chain A and resid 326:333)
20	X-RAY DIFFRACTION	20	(chain A and resid 334:349)

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi