PDB-6k65: Application of anti-helix antibodies in protein structure determi...

ID or keywords:

Entry

Database: PDB / ID: 6k65

Title

Application of anti-helix antibodies in protein structure determination (9014-1P4B)

Components

1P4B variable heavy chain
1P4B variable light chain
Immunoglobulin G-binding 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

Staphylococcus aureus (bacteria)

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.65 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
Revision 1.3	Oct 16, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6k65.cif.gz	131.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6k65.ent.gz	102 KB	Display	PDB format
PDBx/mmJSON format	6k65.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/k6/6k65 ftp://data.pdbj.org/pub/pdb/validation_reports/k6/6k65	HTTPS FTP

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Related structure data

Related structure data	6k3mC 6k64C 6k67C 6k68C 6k69C 6k6aC 6k6bC 1deeS 1p4bS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6g40-3 6pqb-4 6xx7-d 4day-d 2q3j-d 6l1w-d 3h3p-2 5naz-d 5to0-d 6g40-2 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: Immunoglobulin G-binding protein A

L: 1P4B variable light chain

H: 1P4B variable heavy chain

32.9 kDa, 3 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)	35.620, 120.181, 84.740
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-106- HOH
2	1	A-124- HOH

#1: Antibody	Immunoglobulin G-binding protein A / IgG-binding protein A / Staphylococcal protein A / SpA Mass: 8883.901 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (strain NCTC 8325) (bacteria) Strain: NCTC 8325 / Gene: spa, SAOUHSC_00069 / Production host: Escherichia coli (E. coli) / References: UniProt: P02976*PLUS
#2: Antibody	1P4B variable light chain Mass: 11836.013 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: Antibody	1P4B variable heavy chain Mass: 12216.560 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.88 Å³/Da / Density % sol: 57.35 %
Crystal grow	Temperature: 296 K / Method: vapor diffusion, sitting drop / Details: 1.8M NaK phosphate, 0.1M HEPES pH 7.5,

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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: 1.6→50 Å / Num. obs: 44481 / % possible obs: 99.5 % / Redundancy: 5.3 % / R_pim(I) all: 0.032 / Net I/σ(I): 31.8
Reflection shell	Resolution: 1.6→1.7 Å / Num. unique obs: 4320 / R_pim(I) all: 0.22

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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: 1P4B, 1DEE

1p4b

1dee

Resolution: 1.65→36.217 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.06

	R_factor	Num. reflection	% reflection
R_free	0.1918	1999	4.49 %
R_work	0.1699	-	-
obs	0.1708	44477	99.37 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.65→36.217 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2163	0	0	278	2441

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	2207
X-RAY DIFFRACTION	f_angle_d	1	2999
X-RAY DIFFRACTION	f_dihedral_angle_d	18.543	1292
X-RAY DIFFRACTION	f_chiral_restr	0.067	339
X-RAY DIFFRACTION	f_plane_restr	0.007	386

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 (%)
1.6505-1.6918	0.2441	138	0.2285	2918	X-RAY DIFFRACTION	96
1.6918-1.7375	0.2294	137	0.2034	2926	X-RAY DIFFRACTION	98
1.7375-1.7886	0.2238	139	0.1946	2977	X-RAY DIFFRACTION	98
1.7886-1.8463	0.2121	141	0.1844	2981	X-RAY DIFFRACTION	99
1.8463-1.9123	0.2082	141	0.1747	2991	X-RAY DIFFRACTION	100
1.9123-1.9889	0.1911	143	0.1713	3034	X-RAY DIFFRACTION	100
1.9889-2.0794	0.2113	140	0.1577	2987	X-RAY DIFFRACTION	100
2.0794-2.189	0.1562	143	0.1583	3035	X-RAY DIFFRACTION	100
2.189-2.3262	0.213	142	0.1646	3022	X-RAY DIFFRACTION	100
2.3262-2.5057	0.2205	144	0.1703	3054	X-RAY DIFFRACTION	100
2.5057-2.7578	0.2023	145	0.1779	3066	X-RAY DIFFRACTION	100
2.7578-3.1567	0.1915	144	0.1702	3087	X-RAY DIFFRACTION	100
3.1567-3.9763	0.1663	148	0.1552	3126	X-RAY DIFFRACTION	100
3.9763-36.2259	0.1754	154	0.1686	3274	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	5.6607	-2.3943	-0.6564	9.4714	-0.7237	7.5202	-0.2051	-0.5932	-0.2807	0.5933	0.4492	0.0133	0.4924	0.394	-0.3029	0.3562	0.0388	0.0411	0.2196	-0.031	0.2491	1.193	4.492	125.022
2	6.1998	-3.2847	1.6572	8.8335	-2.2386	2.3674	0.5391	0.0585	-0.6951	-0.9624	-0.176	0.0325	0.6862	0.1878	-0.1841	0.3878	0.0962	0.019	0.2524	-0.0463	0.3913	2.869	5.489	113.696
3	3.518	-3.0563	1.9469	6.9274	-3.6242	7.315	-0.1547	-0.0325	-0.0885	0.1265	0.1006	-0.1921	0.1951	0.2303	-0.1204	0.21	-0.0225	0.0317	0.1663	-0.0157	0.1567	1.3205	15.3288	115.42
4	0.6465	0.5814	-0.3922	1.776	-1.0723	3.1675	0.0507	0.1205	-0.0754	0.1693	-0.1135	-0.1137	0.0616	0.3319	0.031	0.126	0.0237	-0.0126	0.1927	-0.0031	0.1333	11.6861	24.9119	94.4611
5	2.4694	-0.7219	1.1988	4.3102	-2.2973	5.8014	0.0263	0.081	0.0094	0.0427	-0.1149	-0.0269	0.0738	-0.0049	-0.0171	0.1156	-0.015	0.0076	0.1472	-0.0126	0.0808	4.2197	26.0914	101.8845
6	3.4063	0.1213	0.8666	2.9573	-1.4203	5.4244	-0.1372	-0.0582	0.7181	-0.2746	-0.2447	0.3973	-0.9383	-0.2077	0.1643	0.3245	0.0156	-0.018	0.2044	0.0074	0.2428	1.615	37.4492	100.6484
7	1.4042	-0.4944	1.7319	1.7443	-2.7349	5.4611	0.0536	-0.1053	-0.0645	0.1171	0.1514	0.217	0.0466	-0.8445	-0.2213	0.1751	-0.0144	0.0009	0.2926	0.0013	0.1263	-4.6656	24.9696	97.1758
8	1.5891	0.0545	1.0065	1.6887	-1.5245	4.6834	0.0612	0.0937	-0.0181	-0.0049	-0.0446	0.0351	0.1091	0.0581	0.0264	0.1082	0.0226	0.0197	0.1672	-0.0142	0.0996	4.9481	26.4269	95.1099
9	3.6615	0.9528	0.1501	2.836	-1.2553	6.5387	0.1298	-0.072	-0.3988	0.1863	-0.1787	-0.1607	0.4661	0.3193	0.1057	0.2135	-0.0059	-0.0186	0.1736	0.0192	0.1507	10.0501	24.0102	111.2654
10	5.2823	-1.2689	3.0777	4.2109	-2.843	2.9072	-0.3255	0.4861	0.5222	-0.0548	-0.2391	-0.3454	-0.1908	0.4169	0.4923	0.1288	-0.0128	-0.004	0.2097	0.0334	0.134	9.8116	34.8386	90.8173
11	9.7376	2.9051	-4.4004	1.6536	-1.0203	2.0967	-0.1073	1.0891	1.505	-0.326	-0.2304	-0.617	0.0584	0.2864	0.3007	0.4338	-0.0371	-0.1064	0.6511	0.2505	0.5511	-4.1374	36.7112	82.2707
12	2.1974	2.0174	1.825	2.2304	1.9314	2.1035	-0.469	0.3255	0.4245	-0.9306	0.1155	0.5754	-0.6794	-0.5161	0.6944	0.3112	0.0178	-0.0761	0.3218	0.0023	0.2688	-7.6326	38.718	111.8708
13	2.7907	-0.5334	-3.2443	7.2302	0.6912	3.7731	0.0072	0.3587	0.3403	0.0008	0.1657	0.9014	-0.8085	0.1262	-0.1639	0.5054	-0.1022	-0.1683	0.496	-0.0855	0.6208	8.0482	48.2151	124.7127
14	4.2065	5.7058	3.4227	8.6336	3.2094	5.0364	-0.2743	0.2326	0.1984	-0.1444	0.2406	0.0445	-0.2007	0.0353	0.047	0.1669	0.0091	0.0021	0.1527	-0.0003	0.1297	-1.4705	39.7836	119.2738
15	2.4855	-2.1294	0.637	4.6678	2.4047	3.8264	-0.1941	0.2547	-0.058	-0.0072	0.0495	0.3985	0.1454	-0.7299	0.0813	0.1614	-0.0572	0.0026	0.2586	0.0048	0.1447	-9.3706	26.691	116.5444
16	1.9048	-1.6539	0.3137	3.6547	-1.6824	3.6247	-0.2742	0.1637	0.2596	-0.6014	0.0337	-0.52	-0.5622	0.5459	0.1817	0.2685	-0.1295	0.0504	0.1882	-0.0023	0.1479	8.8763	36.7012	110.9624
17	2.5743	1.0655	0.2974	3.0134	-0.1653	3.5722	-0.0344	-0.1226	-0.192	0.0216	-0.0119	-0.2048	0.095	0.2241	0.0328	0.1143	0.0143	0.0128	0.114	-0.0124	0.117	6.4135	27.7031	118.4351
18	5.0439	-0.189	1.7711	1.5672	-0.3892	1.9862	-0.0557	-0.1857	0.1403	0.0166	0.0343	0.0419	-0.0909	-0.0339	0.024	0.1269	-0.0002	0.012	0.1168	-0.0074	0.1036	0.9773	34.4397	123.8442
19	4.5237	2.5106	-1.6985	7.7408	-3.0874	1.3704	-0.0562	-0.0186	-0.0491	0.0493	-0.0585	-0.5493	-0.6333	1.4209	0.1803	0.2012	-0.1167	-0.0445	0.3441	0.0079	0.2522	15.6128	42.4548	120.2983
20	8.9094	2.8325	2.6612	6.5603	2.8456	4.2008	-0.2991	0.0036	0.5824	-0.2979	-0.0073	0.1577	-0.5634	-0.1163	0.1167	0.2243	-0.0317	-0.0116	0.1508	0.0024	0.121	4.937	39.4823	111.4928
21	2.3747	0.2889	0.8678	2.1533	2.4071	4.6683	-0.1491	0.1875	0.0752	-0.4827	0.1181	0.1464	-0.2356	-0.3084	0.0979	0.1974	-0.0159	-0	0.2048	0.0186	0.1419	-1.5449	32.7117	107.9513
22	4.2165	3.7508	5.2951	5.8693	2.6953	8.3355	-0.1657	-0.3832	1.3021	0.2838	-0.1836	-0.3433	-0.9664	0.3521	0.4415	0.4371	-0.1044	-0.0661	0.2918	-0.0172	0.3792	11.9032	47.9507	115.9833

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 18 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 19 through 32 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 33 through 61 )
4	X-RAY DIFFRACTION	4	chain 'L' and (resid 6 through 35 )
5	X-RAY DIFFRACTION	5	chain 'L' and (resid 36 through 46 )
6	X-RAY DIFFRACTION	6	chain 'L' and (resid 47 through 55 )
7	X-RAY DIFFRACTION	7	chain 'L' and (resid 56 through 68 )
8	X-RAY DIFFRACTION	8	chain 'L' and (resid 69 through 99 )
9	X-RAY DIFFRACTION	9	chain 'L' and (resid 100 through 105 )
10	X-RAY DIFFRACTION	10	chain 'L' and (resid 106 through 114 )
11	X-RAY DIFFRACTION	11	chain 'L' and (resid 115 through 120 )
12	X-RAY DIFFRACTION	12	chain 'H' and (resid 1 through 7 )
13	X-RAY DIFFRACTION	13	chain 'H' and (resid 8 through 16 )
14	X-RAY DIFFRACTION	14	chain 'H' and (resid 17 through 25 )
15	X-RAY DIFFRACTION	15	chain 'H' and (resid 26 through 33 )
16	X-RAY DIFFRACTION	16	chain 'H' and (resid 34 through 44 )
17	X-RAY DIFFRACTION	17	chain 'H' and (resid 45 through 63 )
18	X-RAY DIFFRACTION	18	chain 'H' and (resid 64 through 82 )
19	X-RAY DIFFRACTION	19	chain 'H' and (resid 83 through 90 )
20	X-RAY DIFFRACTION	20	chain 'H' and (resid 91 through 96 )
21	X-RAY DIFFRACTION	21	chain 'H' and (resid 97 through 106 )
22	X-RAY DIFFRACTION	22	chain 'H' and (resid 107 through 113 )

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