PDB-6k69: Application of anti-helix antibodies in protein structure determi...

ID or keywords:

Entry

Database: PDB / ID: 6k69

Title

Application of anti-helix antibodies in protein structure determination (9213-3LRH)

Components

3LRH intrabody
Engineered T4 lysozyme

Keywords

STRUCTURAL PROTEIN /

antibody /

protein design

Function / homology

Function and homology information

viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process /

lysozyme /

lysozyme activity / host cell cytoplasm / defense response to bacterium
Similarity search - Function

Biological species

Homo sapiens (human)

Enterobacteria phage T4 (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.401 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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PDBx/mmCIF format	6k69.cif.gz	129.5 KB	Display	PDBx/mmCIF format
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Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/k6/6k69 ftp://data.pdbj.org/pub/pdb/validation_reports/k6/6k69	HTTPS FTP

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Related structure data

Related structure data	6k3mC 6k64C 6k65C 6k67C 6k68C 6k6aC 6k6bC 2hukS 3lrhS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1m9e-1 5ttx-3 3ehf-2 6hsm-4 5dor-2 6ono-d 1b7a-d 6hse-1 4dga-1 4zb3-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	#9 - Sep 2000 Lysozyme similarity (6) #100 - Apr 2008 Adrenergic Receptors similarity (6) #136 - Apr 2011 Nanobodies similarity (6) #164 - Aug 2013 Serotonin Receptor similarity (6) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #217 - Jan 2018 Opioid Receptors similarity (4)

Deposited unit

A: 3LRH intrabody

B: Engineered T4 lysozyme

37.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	94.305, 94.305, 101.906
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

#1: Protein	3LRH intrabody Mass: 14203.453 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Protein	Engineered T4 lysozyme Mass: 22870.002 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: P00720*PLUS
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 38 / 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: 3.53 Å³/Da / Density % sol: 70.56 %
Crystal grow	Temperature: 296 K / Method: vapor diffusion, sitting drop / Details: 4.8M Sodium formate, 0.1M Sodium acetate pH 4.5

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Data collection

Diffraction	Mean temperature: 103 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.979 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 23, 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: 2.4→50 Å / Num. obs: 20907 / % possible obs: 100 % / Redundancy: 9.7 % / R_pim(I) all: 0.024 / Net I/σ(I): 19
Reflection shell	Resolution: 2.4→2.5 Å / Num. unique obs: 2071 / R_pim(I) all: 0.203

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3LRH, 2HUK

3lrh

2huk

Resolution: 2.401→43.23 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.86

	R_factor	Num. reflection	% reflection
R_free	0.2344	1991	9.53 %
R_work	0.2043	-	-
obs	0.2073	20901	99.83 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.401→43.23 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2201	0	0	38	2239

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	2238
X-RAY DIFFRACTION	f_angle_d	0.674	3027
X-RAY DIFFRACTION	f_dihedral_angle_d	17.161	1346
X-RAY DIFFRACTION	f_chiral_restr	0.043	341
X-RAY DIFFRACTION	f_plane_restr	0.004	390

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 (%)
2.4007-2.4608	0.3012	139	0.2593	1310	X-RAY DIFFRACTION	98
2.4608-2.5273	0.277	138	0.2489	1337	X-RAY DIFFRACTION	100
2.5273-2.6017	0.2589	141	0.2337	1318	X-RAY DIFFRACTION	100
2.6017-2.6856	0.2805	144	0.2194	1346	X-RAY DIFFRACTION	100
2.6856-2.7816	0.2757	141	0.2288	1340	X-RAY DIFFRACTION	100
2.7816-2.8929	0.2707	135	0.247	1328	X-RAY DIFFRACTION	100
2.8929-3.0246	0.2841	147	0.2304	1338	X-RAY DIFFRACTION	100
3.0246-3.184	0.2772	136	0.2274	1334	X-RAY DIFFRACTION	100
3.184-3.3834	0.2521	145	0.2253	1362	X-RAY DIFFRACTION	100
3.3834-3.6445	0.2509	143	0.2028	1353	X-RAY DIFFRACTION	100
3.6445-4.011	0.2347	143	0.179	1345	X-RAY DIFFRACTION	100
4.011-4.5909	0.1851	145	0.1589	1367	X-RAY DIFFRACTION	100
4.5909-5.7819	0.1841	148	0.1861	1382	X-RAY DIFFRACTION	100
5.7819-43.2367	0.2354	146	0.2218	1450	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	0.1565	-0.0043	-0.5958	5.3027	-1.1729	2.5242	0.8913	0.4342	-0.434	-0.3961	0.5068	0.5725	1.6221	-0.044	0.5273	0.6891	0.1911	-0.6498	1.1438	1.0213	0.7278	-23.4339	-48.966	27.4647
2	2.6606	2.1456	2.9074	4.7071	0.1871	8.1198	0.6593	0.1222	0.0938	0.5753	0.239	-0.5227	-0.0829	0.4661	-0.7212	0.2666	0.0083	0.1238	0.8274	0.1156	0.9226	-41.8879	-41.0649	28.117
3	3.1942	-1.555	0.816	3.2838	0.8745	0.8207	0.0605	-1.2761	-0.353	0.6803	-0.121	-0.5832	0.1807	1.1597	0.0113	0.586	0.0638	-0.1086	1.197	0.2777	0.6506	-20.5622	-43.8395	34.9655
4	2.934	-1.1403	-1.1128	2.8241	-0.7064	4.4079	0.157	-0.3529	-0.2012	0.014	0.0208	0.1717	-0.189	0.2946	-0.1482	0.3077	-0.0106	-0.0724	0.7902	0.0865	0.4837	-26.2899	-35.2249	22.2009
5	8.6257	0.4164	0.0849	9.5746	-3.5065	2.086	-0.1514	-0.7129	0.7396	1.0985	-0.3474	0.0435	-0.454	0.781	0.3036	0.5692	-0.0555	-0.0557	0.8479	0.014	0.6152	-27.0986	-29.1749	31.5143
6	4.7252	-0.9832	4.4763	3.4426	0.1825	4.6254	0.3293	-1.0832	0.1916	0.3128	-0.4739	-0.3508	0.5301	0.7094	0.0837	0.4183	0.0109	-0.0277	1.1822	0.2246	0.537	-27.3335	-39.1628	35.7289
7	7.4984	1.6345	1.4029	0.9539	0.8064	0.8195	-0.3107	0.0618	0.2517	-0.1347	-0.1207	-0.1077	0.0282	1.1283	0.5027	0.3933	-0.0011	-0.0125	1.0093	0.2625	0.5937	-29.1731	-38.2695	25.2644
8	1.4595	-1.3035	2.7421	3.9886	0.0991	7.4414	-0.3891	-0.2564	-0.605	0.2998	0.0805	-0.3343	-0.2422	1.5259	0.0913	0.5377	0.1313	-0.1231	1.2078	0.2289	0.7428	-12.7496	-43.2642	27.7804
9	3.5412	-5.1279	3.5654	9.4775	-2.7531	8.1988	-0.6002	-0.2496	0.1828	0.0575	-0.4301	-0.118	1.1431	-0.0958	1.0316	0.3996	-0.1298	0.0061	0.611	0.0644	0.6399	-37.424	-43.1347	21.9767
10	5.0424	-0.4593	-3.1696	-0.0156	0.3829	7.2579	0.1583	-0.3376	-0.007	0.0089	0.0054	-0.1073	0.2952	0.6496	-0.1282	0.3929	0.0457	-0.0136	0.5167	0.1148	0.61	-2.9267	-42.0073	3.4637
11	6.8185	-3.664	-5.862	5.4183	4.9599	5.855	0.6494	-0.3765	0.2388	0.2196	-0.3322	-0.7351	-0.2195	0.4531	-0.385	0.3929	-0.0825	0.0303	0.7046	0.0857	0.5227	-9.3474	-33.8826	13.0758
12	3.0039	-3.005	-4.9513	5.6741	4.8103	8.6737	0.0723	-0.8318	-0.0276	0.3122	0.0395	-0.5531	0.1936	0.0105	-0.1005	0.317	0.002	-0.0515	0.8341	0.1209	0.6488	-16.9374	-36.0542	18.9168
13	2.8074	0.5994	0.0838	6.3817	-3.7109	7.4814	0.1303	-0.2607	-0.7819	0.1704	0.1509	0.4537	0.1507	-0.1186	-0.2004	0.3166	0.0117	-0.0092	0.4806	0.0711	0.5215	-13.8543	-43.2848	1.4795
14	4.125	-1.6326	1.4897	2.3033	-0.2093	5.6109	-0.035	0.3191	0.4811	-0.4091	-0.3568	-0.158	-0.8565	0.677	0.332	0.6495	-0.0196	-0.0187	0.4885	0.0865	0.5145	-3.7486	-28.4973	-14.2082
15	6.5165	-0.0091	1.1099	4.58	-0.327	5.6523	0.3335	-0.446	0.2421	0.3255	-0.1596	-0.624	-0.6253	0.7427	-0.1644	0.5674	-0.1045	0.0226	0.682	0.1112	0.6223	6.49	-31.3212	-7.8137
16	2.4357	1.0696	0.3809	4.7888	3.8408	3.1857	-0.086	-1.7507	-1.8651	-0.5213	-0.7442	-1.0205	0.9003	3.1881	0.571	0.6737	0.2434	0.1142	1.2039	0.2121	0.9086	5.1102	-44.1758	-11.1384

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 5 through 11 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 12 through 20 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 21 through 36 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 37 through 52 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 53 through 65 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 66 through 79 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 80 through 96 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 97 through 107 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 108 through 113 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 1 through 21 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 22 through 50 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 51 through 72 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 73 through 101 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 102 through 156 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 157 through 177 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 178 through 186 )

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