PDB-6k64: Application of anti-helix antibodies in protein structure determi...

ID or keywords:

Entry

Database: PDB / ID: 6k64

Title

Application of anti-helix antibodies in protein structure determination (8188-3LRH)

Components

3LRH intrabody
Protein A

Keywords

STRUCTURAL PROTEIN / antibody / protein design

Function / homology

Function and homology information

symbiont-mediated suppression of host signal transduction pathway via antagonism of host cell surface receptor / IgG binding / extracellular region
Similarity search - Function

Biological species

Homo sapiens (human)

Staphylococcus aureus subsp. aureus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.933 Å

Authors

Lee, J.O. / Jin, M.S. / Kim, J.W. / Kim, S. / Lee, H. / Cho, G.Y.

Funding support

Korea, Republic Of, 2items

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Application of antihelix antibodies in protein structure determination.
Authors: Kim, J.W. / Kim, S. / Lee, H. / Cho, G. / Kim, S.C. / Lee, H. / Jin, M.S. / Lee, J.O.

History

Deposition	Jun 1, 2019	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Aug 14, 2019	Provider: repository / Type: Initial release
Revision 1.1	Sep 18, 2019	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Nov 22, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6k64.cif.gz	146.6 KB	Display	PDBx/mmCIF format
PDB format	pdb6k64.ent.gz	113.9 KB	Display	PDB format
PDBx/mmJSON format	6k64.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6k64_validation.pdf.gz	444.2 KB	Display	wwPDB validaton report
Full document	6k64_full_validation.pdf.gz	446 KB	Display
Data in XML	6k64_validation.xml.gz	15.6 KB	Display
Data in CIF	6k64_validation.cif.gz	22.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/k6/6k64 ftp://data.pdbj.org/pub/pdb/validation_reports/k6/6k64	HTTPS FTP

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Related structure data

Related structure data	6k3mC 6k65C 6k67C 6k68C 6k69C 6k6aC 6k6bC 1deeS 3lrhS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4p5x-d 6k6a-d 2ff4-2 3qjf-1 6vth-2 1ztp-4 3cjr-d 5xu6-4 6d6i-2 5cup-d 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) #211 - Jul 2017 Pilus Machine similarity (4)

Deposited unit

A: 3LRH intrabody

B: 3LRH intrabody

H: Protein A

C: Protein A

46.1 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	35.061, 41.261, 62.436
Angle α, β, γ (deg.)	85.97, 75.49, 68.26
Int Tables number	1
Space group name H-M	P1

#1: Protein	3LRH intrabody Mass: 14203.453 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Protein	Protein A Mass: 8855.823 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria) Gene: spa / Production host: Escherichia coli (E. coli) / References: UniProt: P02976*PLUS
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	Authors have fused c-terminal of protein A and n-terminal of huntingtin peptides and produced ...Authors have fused c-terminal of protein A and n-terminal of huntingtin peptides and produced engineered protein A. Residues from K51 to Q60 of chain H and residues from K2851 to Q2860 of chain C are originated from huntingtin peptides from 3LRH structure.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1.76 Å³/Da / Density % sol: 30.14 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 35% PEG 4000 0.1M MOPS pH 6.5

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Data collection

Diffraction	Mean temperature: 103 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.979 Å
Detector	Type: MAR CCD 130 mm / Detector: CCD / Date: May 12, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 1.9→50 Å / Num. obs: 22184 / % possible obs: 95.5 % / Redundancy: 3.6 % / R_pim(I) all: 0.032 / Net I/σ(I): 28
Reflection shell	Resolution: 1.9→2 Å / Num. unique obs: 1830 / R_pim(I) all: 0.111

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Processing

Software

Name	Version	Classification
PHENIX	(1.10_2142: ???)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3LRH, 1DEE

3lrh

1dee

Resolution: 1.933→30.439 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 2.03 / Phase error: 22

	R_factor	Num. reflection	% reflection
R_free	0.2068	2018	9.1 %
R_work	0.1708	-	-
obs	0.1742	22183	94.26 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.933→30.439 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2494	0	0	222	2716

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	2536
X-RAY DIFFRACTION	f_angle_d	0.73	3440
X-RAY DIFFRACTION	f_dihedral_angle_d	15.114	1532
X-RAY DIFFRACTION	f_chiral_restr	0.048	386
X-RAY DIFFRACTION	f_plane_restr	0.006	456

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 (%)
1.9335-1.9818	0.2538	96	0.2003	929	X-RAY DIFFRACTION	60
1.9818-2.0354	0.2802	122	0.1887	1417	X-RAY DIFFRACTION	93
2.0354-2.0953	0.247	152	0.1742	1485	X-RAY DIFFRACTION	97
2.0953-2.1629	0.2376	142	0.169	1474	X-RAY DIFFRACTION	97
2.1629-2.2402	0.2151	150	0.174	1469	X-RAY DIFFRACTION	97
2.2402-2.3298	0.218	139	0.1786	1523	X-RAY DIFFRACTION	97
2.3298-2.4358	0.2256	151	0.1742	1474	X-RAY DIFFRACTION	97
2.4358-2.5642	0.2069	148	0.1743	1497	X-RAY DIFFRACTION	98
2.5642-2.7247	0.2267	160	0.1712	1489	X-RAY DIFFRACTION	98
2.7247-2.935	0.2239	148	0.1793	1504	X-RAY DIFFRACTION	98
2.935-3.23	0.1906	145	0.168	1503	X-RAY DIFFRACTION	98
3.23-3.6967	0.2006	150	0.1587	1497	X-RAY DIFFRACTION	98
3.6967-4.6548	0.1633	159	0.1468	1488	X-RAY DIFFRACTION	99
4.6548-30.443	0.2096	156	0.1959	1416	X-RAY DIFFRACTION	93

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	7.4045	-2.33	0.9624	1.134	-0.067	0.2652	-0.8565	0.9489	-0.5337	-0.7296	0.0159	0.6445	0.2409	-0.8762	1.2045	0.3976	-0.1132	0.0277	0.3277	-0.1488	0.3909	-22.485	-2.803	-59.365
2	8.1272	-1.63	0.1075	2.0892	2.4741	8.9338	-0.5217	-0.6631	-0.7209	0.5435	-0.3697	0.5137	0.7582	-0.1689	0.819	0.4041	0.0153	0.0964	0.2775	0.0364	0.4681	-33.308	-2.471	-45.63
3	8.2267	0.293	-6.1336	1.2479	0.1492	4.6384	-0.8349	-0.1994	-0.7067	-0.1727	-0.1401	0.3544	0.4681	-0.1056	1.153	0.2636	0.0239	0.0434	0.1728	0.0209	0.259	-28.226	-1.369	-39.083
4	5.3889	-0.5601	-2.5507	3.8407	1.6422	5.7167	-0.2647	0.1175	-0.0838	-0.3436	0.179	0.0606	0.2322	0.2396	0.0449	0.1827	-0.0046	0.0272	0.097	0.0078	0.1777	-14.139	-1.629	-55.146
5	9.4973	-2.8667	3.4695	2.0559	-0.8316	1.9039	0.0939	-0.7525	0.5328	0.1918	0.4467	1.1548	-0.6337	-0.9047	-0.3649	0.2562	0.1432	-0.0509	0.339	0.1086	0.5102	-28.483	12.673	-51.974
6	1.7651	0.9951	-1.5884	1.5015	1.0882	5.3936	-0.0891	-0.1484	-0.0717	0.1393	0.0472	0.0041	0.2012	0.214	0.0666	0.1311	0.0594	-0.0031	0.1249	0.0177	0.1707	-17.1716	3.8576	-44.5853
7	4.1751	0.5753	-3.3365	2.4117	-0.1459	6.1449	-0.2843	0.1299	0.0179	-0.1663	0.1389	0.2365	0.174	-0.2803	0.1419	0.129	0.0066	-0.0388	0.1011	0.0009	0.1727	-24.1049	4.0049	-52.7367
8	1.5688	0.9024	0.7557	2.9258	-1.6452	2.3226	0.2773	-0.088	0.1288	0.1767	-0.2447	0.2328	-0.8835	0.411	0.1148	0.3055	-0.0553	0.0055	0.2331	0.0039	0.1928	-19.5713	23.2567	-23.4581
9	3.9236	0.2487	-1.7838	5.5154	0.1942	6.4618	0.1366	0.1809	-0.1459	-0.0441	-0.0151	0.2954	-0.1249	0.1345	-0.0902	0.0839	0.0003	0.0044	0.106	0.004	0.1385	-24.2138	13.7539	-16.5802
10	1.3819	0.3728	-1.2249	2.6752	-1.5604	2.954	0.1198	-0.0102	0.03	-0.0512	-0.0783	0.0203	-0.1072	0.2888	-0.0312	0.0983	-0.0098	-0.0222	0.1697	-0.0225	0.1169	-21.2889	14.9425	-19.8114
11	5.5732	-2.3131	-0.2878	2.0872	-0.8256	6.8523	-0.536	-0.7814	-0.9645	0.1081	0.5487	-0.0104	0.3269	0.9196	0.0145	0.2252	0.0129	0.0633	0.3667	0.066	0.3488	-21.8299	-14.8401	-15.0474
12	6.5949	-0.3904	-1.416	8.812	1.8282	6.4082	-0.2956	0.1271	-0.642	0.1844	0.0428	0.6093	0.0848	-0.5648	0.2704	0.1241	-0.0064	0.0321	0.1853	-0.0073	0.2673	-29.5526	-3.0481	-15.0159
13	9.994	-4.9745	-0.7637	2.527	0.2196	6.7097	-0.0144	0.9926	-0.6491	-0.425	-0.5349	-0.0539	0.6946	-0.0705	0.6039	0.3445	0.0126	0.0826	0.2707	0.0221	0.2725	-22.4519	-7.4453	-23.5952
14	5.1684	-1.98	-1.1637	3.2798	0.7775	4.9665	0.0346	-0.0168	0.034	0.0229	-0.107	-0.3178	0.1708	0.2476	-0.0101	0.1213	0.0115	0.0031	0.1367	0.0366	0.1812	-22.1038	0.1075	-14.7323
15	5.3871	3.237	0.9381	3.3112	1.8366	2.8229	-0.254	-0.0566	0.764	-0.1423	0.1839	-1.0335	-0.4023	0.7266	0.1329	0.7164	-0.1487	-0.1614	0.4984	0.139	0.734	3.4855	25.6123	-42.4294
16	5.1697	4.0505	-0.1938	4.1388	2.0074	5.0815	0.3432	-0.0026	-0.4929	1.0309	-0.9267	-0.7173	0.1778	0.2486	0.4731	0.397	-0.1269	-0.0166	0.2332	0.0755	0.2726	-4.0674	25.6077	-47.9659
17	4.1622	-0.1165	-0.7583	7.856	0.849	7.7004	0.0469	0.232	0.3662	-0.0675	0.0321	-0.202	-0.6273	0.3323	0.0501	0.2004	-0.0223	-0.0001	0.1705	0.0277	0.1685	-11.5542	21.3213	-53.7682
18	8.2256	1.7022	3.6898	6.1362	2.0782	2.1632	-0.1367	-0.2165	0.4029	0.2164	-0.1604	-0.0665	-0.6347	0.053	0.2971	0.3176	-0.0215	0.0413	0.1914	0.009	0.2359	-11.4133	22.6841	-42.0159
19	6.0639	0.8846	2.9539	5.2362	0.5809	6.2777	-0.0157	-0.2873	-0.2395	0.3956	-0.02	-0.5658	-0.1381	0.2894	0.0379	0.138	-0.0067	-0.0006	0.1622	0.0316	0.1753	-6.4491	15.3702	-46.3111
20	2.0805	2.6567	3.3343	8.0092	3.5069	9.6196	0.537	0.6156	1.3393	-0.8926	0.023	0.6246	0.3544	-0.5542	-0.4352	0.287	-0.024	0.0031	0.2849	0.0418	0.2873	-19.1128	12.0451	-60.2765

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 5 through 9 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 10 through 17 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 18 through 23 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 24 through 39 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 40 through 49 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 50 through 76 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 77 through 113 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 5 through 23 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 24 through 49 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 50 through 113 )
11	X-RAY DIFFRACTION	11	chain 'H' and (resid 4 through 15 )
12	X-RAY DIFFRACTION	12	chain 'H' and (resid 16 through 21 )
13	X-RAY DIFFRACTION	13	chain 'H' and (resid 22 through 35 )
14	X-RAY DIFFRACTION	14	chain 'H' and (resid 36 through 59 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 2804 through 2808 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 2809 through 2815 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 2816 through 2821 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 2822 through 2835 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 2836 through 2853 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 2854 through 2859 )

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