PDB-5h76: Crystal structure of the DARPin-Protein A fusion protein

ID or keywords:

Entry

Database: PDB / ID: 5h76

Title

Crystal structure of the DARPin-Protein A fusion protein

Components

DARPin,Immunoglobulin G-binding protein A

Keywords

IMMUNE SYSTEM / synthetic protein

Function / homology

Function and homology information

IgG binding / extracellular region
Similarity search - Function

Biological species

synthetic construct (others)

Staphylococcus aureus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.6 Å

Authors

Youn, S.J. / Kwon, N.Y. / Lee, J.H. / Kim, J.H. / Lee, H. / Lee, J.O.

Citation

Journal: Sci Rep / Year: 2017
Title: Construction of novel repeat proteins with rigid and predictable structures using a shared helix method.
Authors: Youn, S.J. / Kwon, N.Y. / Lee, J.H. / Kim, J.H. / Choi, J. / Lee, H. / Lee, J.O.

History

Deposition	Nov 17, 2016	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jun 28, 2017	Provider: repository / Type: Initial release
Revision 1.1	Mar 20, 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

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5h76.cif.gz	238.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5h76.ent.gz	196.2 KB	Display	PDB format
PDBx/mmJSON format	5h76.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5h76_validation.pdf.gz	440.5 KB	Display	wwPDB validaton report
Full document	5h76_full_validation.pdf.gz	445 KB	Display
Data in XML	5h76_validation.xml.gz	23 KB	Display
Data in CIF	5h76_validation.cif.gz	31.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h7/5h76 ftp://data.pdbj.org/pub/pdb/validation_reports/h7/5h76	HTTPS FTP

-
Related structure data

Related structure data	5h75C 5h77C 5h78C 5h79C 5h7aC 5h7bC 5h7cC 5h7dC 5x3fC 5xbyC C: citing same article (ref.)
Similar structure data	5y4e-1 4r58-3 4g5a-d 5cea-4 6prq-d 5cea-3 5ko4-d 3ggy-2 1in0-2 4r58-1 Search similar-shape structures by Omokage search (details) 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

Related structure data

C: citing same article (ref.)

Similar structure data

-
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: DARPin,Immunoglobulin G-binding protein A

B: DARPin,Immunoglobulin G-binding protein A

C: DARPin,Immunoglobulin G-binding protein A

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

1

A: DARPin,Immunoglobulin G-binding protein A

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

2

B: DARPin,Immunoglobulin G-binding protein A

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

3

C: DARPin,Immunoglobulin G-binding protein A

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

Unit cell

Length a, b, c (Å)	70.753, 94.684, 70.916
Angle α, β, γ (deg.)	90.00, 117.29, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Antibody	DARPin,Immunoglobulin G-binding protein A / IgG-binding protein A / Staphylococcal protein A Mass: 21772.359 Da / Num. of mol.: 3 / Fragment: RESIDUES 9-176,177-209 (UNP RESIDUES 235-267) / Mutation: G182A Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others), (gene. exp.) Staphylococcus aureus (bacteria) Gene: spa / Production host: Escherichia coli (E. coli) / References: UniProt: P38507
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H₂O

#1: Antibody

DARPin,Immunoglobulin G-binding protein A / IgG-binding protein A / Staphylococcal protein A

Mass: 21772.359 Da / Num. of mol.: 3 / Fragment: RESIDUES 9-176,177-209 (UNP RESIDUES 235-267) / Mutation: G182A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others), (gene. exp.)

Staphylococcus aureus (bacteria)
Gene: spa / Production host:

Escherichia coli (E. coli) / References: UniProt: P38507

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 152 / 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: 3.29 Å³/Da / Density % sol: 62.67 %
Crystal grow	Temperature: 296 K / Method: vapor diffusion / pH: 9.5 / Details: 0.63M sodium potassium phosphate pH 9.5

-
Data collection

Diffraction	Mean temperature: 80 K
Diffraction source	Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 22, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97934 Å / Relative weight: 1
Reflection	Resolution: 2.6→50 Å / Num. obs: 27769 / % possible obs: 99.6 % / Redundancy: 3.4 % / Net I/σ(I): 9.9
Reflection shell	Resolution: 2.6→2.69 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.22 / % possible all: 99.6

-
Processing

Software

Name	Version	Classification
PHENIX	1.10.1_2155	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
PHASER		phasing

Refinement

Resolution: 2.6→33.172 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 27.07

	R_factor	Num. reflection	% reflection
R_free	0.2499	2003	7.77 %
R_work	0.2164	-	-
obs	0.219	25768	99.16 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.6→33.172 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4512	0	0	152	4664

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	4590
X-RAY DIFFRACTION	f_angle_d	0.563	6237
X-RAY DIFFRACTION	f_dihedral_angle_d	12.134	2736
X-RAY DIFFRACTION	f_chiral_restr	0.037	714
X-RAY DIFFRACTION	f_plane_restr	0.005	828

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 (%)
2.5897-2.6545	0.3269	161	0.3034	1569	X-RAY DIFFRACTION	94
2.6545-2.7262	0.3061	126	0.2971	1735	X-RAY DIFFRACTION	99
2.7262-2.8064	0.3225	144	0.2888	1698	X-RAY DIFFRACTION	100
2.8064-2.8969	0.3184	130	0.2755	1671	X-RAY DIFFRACTION	99
2.8969-3.0004	0.3245	147	0.2584	1701	X-RAY DIFFRACTION	100
3.0004-3.1204	0.3135	149	0.2572	1697	X-RAY DIFFRACTION	100
3.1204-3.2623	0.2811	147	0.2408	1691	X-RAY DIFFRACTION	100
3.2623-3.4342	0.2842	144	0.241	1689	X-RAY DIFFRACTION	99
3.4342-3.6491	0.286	137	0.2183	1713	X-RAY DIFFRACTION	100
3.6491-3.9304	0.2202	130	0.1924	1750	X-RAY DIFFRACTION	100
3.9304-4.3252	0.2066	135	0.1678	1696	X-RAY DIFFRACTION	100
4.3252-4.9493	0.1796	148	0.1604	1700	X-RAY DIFFRACTION	99
4.9493-6.2288	0.2709	151	0.221	1712	X-RAY DIFFRACTION	100
6.2288-33.1751	0.1582	154	0.1655	1743	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	6.332	-2.8699	-1.8884	2.7113	-0.3309	2.9999	0.3253	0.7582	0.6742	-1.017	-0.3966	-0.8472	-0.3796	-0.0276	-0.0985	0.2882	-0.019	0.0559	0.3431	0.0063	0.325	32.8073	34.5715	136.0313
2	4.3652	-0.2184	-0.447	7.3519	-0.7318	4.1046	-0.3469	-0.4955	0.6344	-0.0625	0.2256	-0.4118	-0.4505	0.1707	-0.2405	0.3314	-0.0891	-0.0279	0.2327	-0.0433	0.3201	33.6807	33.7227	141.4524
3	3.664	-1.3863	0.2061	6.9008	-0.5584	5.3843	0.3262	-0.0181	0.0269	-0.3282	0.4665	-0.5543	-0.0929	-0.1699	-0.1657	0.2518	-0.0668	-0.0101	0.2483	0.0143	0.2756	35.4762	24.5049	142.5776
4	5.623	-0.0247	1.5347	6.349	0.2596	6.7069	-0.7151	-0.1826	0.1573	-0.1622	0.2594	0.5789	0.0139	-0.9996	-0.6756	0.2952	-0.0096	-0.0377	0.3534	0.1997	0.3284	24.1418	23.8074	144.6218
5	2.2051	1.8689	0.1816	3.6989	-0.1168	2.699	-0.2103	-0.2905	-0.1431	-0.1523	0.5018	0.4669	0.4447	-0.274	-0.2063	0.3861	-0.062	-0.0724	0.3757	0.1771	0.3252	26.1247	8.9029	143.1765
6	3.9065	-0.9745	-2.4537	4.655	-1.4771	2.5954	-0.3964	0.6546	0.8789	-0.0467	-0.0068	-1.2837	0.2178	0.0523	0.1154	0.4586	-0.1165	-0.1351	0.4005	0.0979	0.4779	27.5479	-4.5273	147.3349
7	6.393	0.9768	1.6931	7.9159	-5.2965	4.9903	-0.546	0.1091	-0.1852	-0.8024	0.519	-0.6294	0.6849	0.0484	0.1696	0.3246	-0.0194	0.0155	0.304	-0.058	0.3563	26.6641	-13.3756	153.9192
8	4.7859	0.9169	-0.4292	4.9804	-1.3234	3.3376	-0.68	0.4304	-0.5182	-1.2312	0.3412	0.2356	0.4911	-0.2944	0.0524	0.7699	-0.1959	-0.2077	0.3281	0.0764	0.4544	19.0828	-12.7794	148.9584
9	9.0063	2.4666	-4.2911	7.8806	-3.4065	9.7623	-0.9508	1.2095	-0.7854	-1.2707	-0.5957	-0.519	0.6349	0.1031	0.6356	0.5469	0.1017	-0.0575	0.4125	0.1328	0.5715	30.4834	-2.0099	108.2277
10	3.1603	-2.5232	-0.5672	3.6616	-0.805	5.4477	0.5164	-0.5207	-0.8504	0.8212	-0.2841	-0.1207	1.0522	-0.1176	-0.043	0.6685	-0.0314	-0.0919	0.3084	0.0487	0.827	33.1818	-6.0097	117.228
11	7.7294	-1.3528	0.2616	0.7052	0.8312	3.2807	0.4005	0.2034	-0.4563	-0.0525	-0.4539	-0.0445	-0.2824	0.2037	0.0206	0.4073	-0.0235	-0.1072	0.219	0.0646	0.453	30.3068	4.1518	114.8234
12	4.8441	-1.7646	0.1903	5.0222	-0.2027	1.0793	0.6782	0.6838	-0.1623	-0.7157	-0.8756	0.2966	-0.0124	0.3733	0.0846	0.6173	0.0418	-0.0584	0.375	0.1494	0.3594	29.5761	13.1806	112.7455
13	5.4526	-1.5034	1.5523	4.2858	1.1747	2.8102	0.1498	0.0148	0.1454	-0.1092	-0.2576	0.0681	-0.3008	0.0728	0.2034	0.3936	-0.0252	-0.0837	0.1705	0.0145	0.2186	19.6094	15.5361	120.5493
14	1.9731	-1.747	0.0551	2.3763	0.8106	1.9739	0.021	0.1522	-0.1375	-0.4224	-0.1215	0.264	-0.1341	-0.1869	0.1501	0.5424	-0.0451	-0.0739	0.272	-0.0613	0.3007	11.3061	25.7883	122.436
15	1.723	-2.3483	-1.8451	3.626	1.656	8.095	-0.4564	-0.4039	-0.7683	0.7454	-0.1165	0.5956	0.4343	-0.1069	0.4868	0.6139	0.0669	-0.015	0.2887	-0.006	0.5029	7.8876	34.0341	136.4816
16	5.6257	3.6963	-0.4184	4.9569	0.8955	3.5601	-0.2852	0.3174	0.521	-0.4205	-0.1435	1.6717	-0.2404	-0.2073	0.2838	0.484	0.0788	-0.1388	0.3318	-0.0929	0.5231	5.9242	37.1725	128.0983
17	6.205	0.8683	-0.9384	5.8602	-1.0672	6.2302	0.0061	-0.3576	0.2651	-0.1234	0.3206	1.2984	-0.1718	-0.3742	-0.1422	0.531	0.047	0.0039	0.309	-0.0772	0.3443	-13.3509	6.2607	111.5081
18	5.0214	0.7705	0.1944	4.2442	-0.9205	4.1202	0.0941	0.4358	-0.1369	0.119	0.0579	0.0519	0.1888	-0.2882	-0.1268	0.2765	0.0191	-0.0377	0.2488	-0.0218	0.2622	-3.7698	3.3975	106.0111
19	4.8692	0.2005	-2.0072	2.6371	-1.5988	4.2045	0.0557	0.6973	-0.2312	0.0739	0.0804	-0.4995	0.1291	-0.0008	-0.1364	0.276	0.0201	-0.1238	0.3422	-0.0328	0.3876	9.7246	9.6815	95.6538
20	8.1159	-5.0698	4.2425	9.7658	-4.3971	3.0828	-0.0764	0.0377	0.8283	-0.2111	-0.5584	-0.4768	0.0951	0.3174	0.2481	0.3437	0.0199	-0.0638	0.7058	0.0947	0.3817	22.2748	15.4566	92.9944
21	8.7049	4.0867	0.9162	2.2861	1.7381	5.4579	0.4741	1.2303	0.7853	0.1901	-0.7243	-1.0134	-0.0842	1.5038	-0.0186	0.6106	0.0397	0.08	0.8788	0.0806	0.6328	33.3479	16.0725	92.5722
22	2.2605	1.3277	-0.8369	3.6269	2.5587	5.9503	-0.0136	1.427	0.4175	-0.778	0.3567	-1.4727	0.1949	0.9359	-0.0403	0.3929	-0.124	0.1068	1.1104	0.0575	0.5216	30.306	12.5551	84.6539

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 13 through 24 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 25 through 49 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 50 through 68 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 69 through 82 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 83 through 157 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 158 through 171 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 172 through 190 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 191 through 209 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 13 through 24 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 25 through 35 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 36 through 68 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 69 through 82 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 83 through 134 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 135 through 171 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 172 through 190 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 191 through 209 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 13 through 35 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 36 through 82 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 83 through 157 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 158 through 171 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 172 through 190 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 191 through 209 )

-
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