PDB-5x2d: Crystal structure of DLC like domain of CsTAL3 (83-177aa)

ID or keywords:

Entry

Database: PDB / ID: 5x2d

Title

Crystal structure of DLC like domain of CsTAL3 (83-177aa)

Components

Tegumental protein 20.8 kDa

Keywords

CELL ADHESION / Calcium-binding protein / Tegument protein / CsTAL3 / Dynein light chain

Function / homology

Function and homology information

dynein complex / microtubule-based process / calcium ion binding
Similarity search - Function

Biological species

Clonorchis sinensis (oriental liver fluke)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.6 Å

Authors

Jo, C.H. / Hwang, K.Y.

Funding support

Korea, Republic Of, 1items

Citation

Journal: Sci Rep / Year: 2017
Title: Structural insights into a 20.8-kDa tegumental-allergen-like (TAL) protein from Clonorchis sinensis
Authors: Jo, C.H. / Son, J. / Kim, S. / Oda, T. / Kim, J. / Lee, M.R. / Sato, M. / Kim, H.T. / Unzai, S. / Park, S.Y. / Hwang, K.Y.

History

Deposition	Jan 31, 2017	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Aug 30, 2017	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 2017	Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2	Mar 27, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3	Apr 3, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5x2d.cif.gz	130.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5x2d.ent.gz	105.7 KB	Display	PDB format
PDBx/mmJSON format	5x2d.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5x2d_validation.pdf.gz	443.6 KB	Display	wwPDB validaton report
Full document	5x2d_full_validation.pdf.gz	448.2 KB	Display
Data in XML	5x2d_validation.xml.gz	12.2 KB	Display
Data in CIF	5x2d_validation.cif.gz	16.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x2/5x2d ftp://data.pdbj.org/pub/pdb/validation_reports/x2/5x2d	HTTPS FTP

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Related structure data

Related structure data	5x2eC C: citing same article (ref.)
Similar structure data	3r0h-2 2b3s-2 5csi-d 2b3s-1 4e9m-8 1vaj-d 3r0h-4 5csf-d 3r0h-1 4m2p-d Search similar-shape structures by Omokage search (details) 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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Tegumental protein 20.8 kDa

B: Tegumental protein 20.8 kDa

C: Tegumental protein 20.8 kDa

32.4 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Tegumental protein 20.8 kDa

C: Tegumental protein 20.8 kDa

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

2

B: Tegumental protein 20.8 kDa

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

Unit cell

Length a, b, c (Å)	88.397, 154.082, 61.631
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

#1: Protein	Tegumental protein 20.8 kDa / CsTAL3 Mass: 10800.202 Da / Num. of mol.: 3 Fragment: Dynein light chain like domain, UNP residues 83-177 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clonorchis sinensis (oriental liver fluke) Production host: Escherichia coli (E. coli) / References: UniProt: Q2PMV7
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 19 / 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: 3.24 Å³/Da / Density % sol: 62.02 %
Crystal grow	Temperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 170 mM MgSO4, 21 % PEG 3350

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

Photon Factory

/ Beamline: BL-1A / Wavelength: 1.1 Å

Detector

Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 16, 2016

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.1 Å / Relative weight: 1

Reflection

Resolution: 2.6→50 Å / Num. obs: 12758 / % possible obs: 95.2 % / Redundancy: 8.2 % / B_iso Wilson estimate: 60.29 Å² / R_merge(I) obs: 0.089 / R_pim(I) all: 0.03 / R_rim(I) all: 0.095 / Χ²: 1.875 / Net I/σ(I): 11.3

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.6-2.64	5.2	0.304	0.858	0.125	0.331	0.35	84.3
2.64-2.69	5.6	0.726	0.009	0.319	0.799	6.604	85.5
2.69-2.74	5.9	0.303	0.91	0.119	0.327	0.662	87.3
2.74-2.8	6.1	0.288	0.077	0.124	0.316	0.842	88.4
2.8-2.86	6.7	0.321	0.916	0.129	0.348	1.087	92.8
2.86-2.93	7	0.186	0.976	0.068	0.199	0.455	91.8
2.93-3	7	0.149	0.988	0.053	0.158	0.45	95.2
3-3.08	7	0.164	0.981	0.059	0.175	0.477	95.5
3.08-3.17	7.2	0.129	0.993	0.046	0.138	0.521	97.1
3.17-3.28	7.7	0.278	0.861	0.097	0.295	2.064	96.2
3.28-3.39	8.2	0.086	0.997	0.028	0.091	0.775	98.2
3.39-3.53	8.6	0.501	0.954	0.153	0.524	4.373	98.5
3.53-3.69	8.7	0.188	0.937	0.064	0.199	3.731	98.5
3.69-3.88	8.1	0.099	0.998	0.035	0.106	1.786	97.6
3.88-4.13	8.2	0.141	0.998	0.049	0.149	4.166	98.9
4.13-4.45	9.6	0.043	0.999	0.014	0.045	1.531	99.6
4.45-4.89	10.7	0.041	0.999	0.013	0.043	1.624	99.6
4.89-5.6	12	0.037	0.999	0.011	0.038	1.402	100
5.6-7.05	11.8	0.034	0.999	0.01	0.035	1.315	99.6
7.05-50	10.9	0.037	0.99	0.014	0.039	2.565	99.1

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Processing

Software

Name	Version	Classification
PHENIX	1.8.3_1479	refinement
HKL-2000		data scaling
PHENIX	1.8.3_1479	model building
HKL-2000		data reduction
PHENIX	1.8.3_1479	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: SAD structure

Resolution: 2.6→48.126 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 33.56 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2674	1278	10.07 %
R_work	0.2237	-	-
obs	0.228	12685	95.08 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.6→48.126 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2280	0	0	19	2299

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	2340
X-RAY DIFFRACTION	f_angle_d	1.582	3183
X-RAY DIFFRACTION	f_dihedral_angle_d	15.723	846
X-RAY DIFFRACTION	f_chiral_restr	0.073	351
X-RAY DIFFRACTION	f_plane_restr	0.008	405

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 (%)
2.6002-2.7043	0.3796	119	0.3682	1105	X-RAY DIFFRACTION	84
2.7043-2.8274	0.3573	121	0.3241	1157	X-RAY DIFFRACTION	89
2.8274-2.9764	0.3502	142	0.3077	1235	X-RAY DIFFRACTION	93
2.9764-3.1628	0.3637	141	0.3119	1257	X-RAY DIFFRACTION	96
3.1628-3.407	0.3032	146	0.2537	1280	X-RAY DIFFRACTION	97
3.407-3.7497	0.2534	147	0.2246	1292	X-RAY DIFFRACTION	99
3.7497-4.292	0.2505	146	0.1883	1324	X-RAY DIFFRACTION	99
4.292-5.4063	0.1966	150	0.183	1350	X-RAY DIFFRACTION	100
5.4063-48.1345	0.2668	166	0.2038	1407	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	5.1099	2.5357	-0.7996	7.5978	-3.8793	5.9901	0.6263	-1.2775	-1.2257	0.659	-0.0916	0.0442	0.768	-0.5009	-0.3634	0.9575	-0.11	-0.596	0.9035	0.5136	1.26	-6.5817	-31.9271	-5.5342
2	2.2334	-0.9181	0.934	1.267	0.0983	2.3751	-0.0666	-0.9724	-0.618	0.6497	0.3102	0.4165	0.5147	-1.0873	-0.4684	0.9986	-0.2952	-0.2521	1.2177	0.728	0.9409	-15.4486	-28.1807	-2.4717
3	3.109	2.583	0.1896	4.6714	0.2229	2.8944	0.8566	-1.683	0.0485	0.8256	-0.4157	0.804	0.3743	-1.5617	-0.3443	0.7314	-0.0517	0.1572	1.1388	0.4865	0.6945	-20.9134	-20.5706	-7.0242
4	8.9762	7.5264	3.8001	7.4929	5.0212	8.6948	0.53	-0.0673	0.1107	-0.2277	0.0769	0.5531	0.0267	-0.3637	-0.2009	0.5047	-0.1695	-0.2451	0.7173	0.6025	1.1989	-15.0131	-20.704	-12.8732
5	1.4443	0.6589	1.072	2.4569	0.0772	2.0985	0.5281	0.1709	-0.8637	-0.0949	0.2788	0.581	0.8255	-0.3174	-0.5613	0.654	0.0589	-0.5194	0.7186	0.2071	1.4511	-8.0546	-26.8416	-20.329
6	1.6875	-0.0505	-0.1838	5.5438	-4.3633	5.3463	0.4593	-0.006	-0.6378	-0.4644	0.0893	0.613	0.8735	-0.5513	-0.822	0.8311	-0.1115	-0.5295	0.6584	0.4829	1.1446	-12.8626	-32.7319	-9.9185
7	6.5441	5.0235	-0.0016	8.1543	-1.1475	5.914	0.4401	0.2314	-0.0006	-0.1413	0.0998	0.178	0.0555	-0.0897	-0.3107	0.5628	-0.1441	-0.2856	0.7135	0.5322	1.2016	-12.5109	-22.5002	-12.474
8	3.7263	5.1313	-2.5089	9.1292	-2.005	3.1872	0.403	-0.775	-0.2002	0.9706	0.0965	0.5777	-0.2906	-0.2865	-0.4347	0.9664	0.2673	0.3267	1.7112	0.958	1.4453	-34.4275	-10.2585	-10.8232
9	2.7838	1.0103	-1.6366	2.0204	-0.2346	2.1182	0.2915	-0.4674	0.1267	0.5854	0.3032	0.7719	-0.56	-0.5561	-0.3509	0.7926	0.0101	0.3618	1.0426	0.6899	0.9369	-28.6975	-5.3133	-14.1538
10	2.2312	-4.0788	1.6607	7.4557	-3.0356	1.2359	-0.27	-0.5252	0.0804	0.4761	0.7605	0.5181	-0.6149	-1.061	-0.4931	1.0513	0.6695	0.3427	1.5609	0.517	1.6321	-41.7443	7.3586	-18.4376
11	5.1907	0.2422	-1.5451	2.3344	-0.7048	1.7094	-0.4951	-1.3048	1.4443	1.0559	0.9335	0.4088	-1.4714	-1.1551	-0.385	1.242	0.3484	0.5235	1.0203	0.154	0.9581	-28.6728	8.4698	-17.5636
12	3.0664	-1.0489	0.3083	0.7337	0.6572	1.8818	0.5986	-0.0992	0.2291	-0.1854	0.3636	0.5683	0.0377	-0.7954	-0.205	0.6466	0.1286	0.1354	0.6564	0.7121	1.2584	-26.0199	-2.9508	-27.1047
13	2.1836	1.0109	-1.1664	2.7691	-1.6854	2.8014	0.1364	0.0746	0.204	-0.1671	0.3841	0.5279	-0.1425	-0.6788	-0.2656	0.4994	-0.0911	0.2513	0.8024	0.7449	1.1032	-29.6314	-2.4555	-21.5195
14	4.6098	2.1267	2.2276	1.7547	3.0974	7.4083	-0.104	0.6728	-0.0886	-0.5111	0.2328	0.3662	0.1655	0.0243	-0.0888	1.4831	-0.3128	-0.8877	1.0462	0.0987	1.4986	-26.3587	-24.6608	-41.4765
15	3.1725	0.5817	1.0598	1.6894	1.2802	2.4694	0.4309	0.6376	-0.6512	-0.451	0.1238	0.3073	0.7756	0.2044	-0.3148	0.966	-0.0267	-0.7102	0.7469	0.136	0.91	-19.1371	-22.4963	-37.281
16	4.6286	-4.3478	3.3114	4.9542	-3.6336	2.6836	0.4095	0.4391	-0.5489	-2.0222	0.0429	-0.0885	1.9401	0.1295	-0.4608	2.1798	0.0741	-0.7197	0.7214	-0.102	1.7092	-14.4812	-40.0731	-32.861
17	5.2454	4.1965	0.3119	8.6308	1.4662	2.1385	0.4748	0.3532	-1.1059	-1.799	-0.1678	-1.2634	1.599	0.5651	-0.2987	1.1795	0.3156	-0.4802	0.816	-0.3592	0.9532	-7.0236	-29.1862	-33.8297
18	3.0841	2.9119	-3.573	6.2086	-3.9479	7.1117	0.3222	-0.1578	-0.1741	-0.0669	0.2345	0.0356	0.2299	0.3666	-0.071	0.7514	0.0382	-0.611	0.4356	-0.0917	0.9212	-10.3464	-22.5299	-29.4648
19	1.2501	1.061	0.2176	1.5697	0.1212	1.129	0.5279	-0.1391	-0.9236	-0.0872	0.3942	0.3272	0.8174	-0.6168	-0.5639	0.692	0.0201	-0.4232	0.7354	0.4146	1.3881	-19.1187	-20.4357	-20.7525
20	3.8421	0.5472	2.139	1.8078	0.0962	3.5181	0.3254	-0.1006	-0.6131	0.0162	0.2479	0.1218	0.753	-0.3788	-0.3653	0.8434	-0.1304	-0.7648	0.6495	0.1417	1.0667	-16.9235	-24.5148	-29.8354

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 83 through 97 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 98 through 117 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 118 through 136 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 137 through 145 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 146 through 159 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 160 through 167 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 168 through 177 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 83 through 89 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 90 through 112 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 113 through 117 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 118 through 135 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 136 through 159 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 160 through 177 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 83 through 88 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 89 through 112 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 113 through 117 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 118 through 135 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 136 through 145 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 146 through 159 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 160 through 177 )

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