PDB-8ojs: Crystal structure of the human IgD Fab - structure Fab1

ID or keywords:

Entry

Database: PDB / ID: 8ojs

Title

Crystal structure of the human IgD Fab - structure Fab1

Components

Human IgD Fab heavy chain
Human IgD Fab light chain

Keywords

IMMUNE SYSTEM / Fab / Antibody / Immunoglobulin

Function / homology

PHOSPHATE ION

Function and homology information

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.75 Å

Authors

Davies, A.M. / Beavil, R.L. / McDonnell, J.M.

Funding support

United Kingdom, 1items

Citation

Journal: Mol.Immunol. / Year: 2023
Title: Crystal structures of the human IgD Fab reveal insights into C H 1 domain diversity.
Authors: Davies, A.M. / Beavil, R.L. / Barbolov, M. / Sandhar, B.S. / Gould, H.J. / Beavil, A.J. / Sutton, B.J. / McDonnell, J.M.

History

Deposition	Mar 24, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 14, 2023	Provider: repository / Type: Initial release
Revision 1.1	Oct 16, 2024	Group: Data collection / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8ojs.cif.gz	349.4 KB	Display	PDBx/mmCIF format
PDB format	pdb8ojs.ent.gz	287.7 KB	Display	PDB format
PDBx/mmJSON format	8ojs.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8ojs_validation.pdf.gz	470.1 KB	Display	wwPDB validaton report
Full document	8ojs_full_validation.pdf.gz	477.2 KB	Display
Data in XML	8ojs_validation.xml.gz	31.8 KB	Display
Data in CIF	8ojs_validation.cif.gz	42.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oj/8ojs ftp://data.pdbj.org/pub/pdb/validation_reports/oj/8ojs	HTTPS FTP

-
Related structure data

Related structure data	8ojtC 8ojuC 8ojvC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
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)

Deposited unit

A: Human IgD Fab light chain

B: Human IgD Fab heavy chain

L: Human IgD Fab light chain

H: Human IgD Fab heavy chain

hetero molecules

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

1

A: Human IgD Fab light chain

B: Human IgD Fab heavy chain

hetero molecules

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

2

L: Human IgD Fab light chain

H: Human IgD Fab heavy chain

hetero molecules

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

Unit cell

Length a, b, c (Å)	43.534, 71.789, 90.861
Angle α, β, γ (deg.)	92.52, 91.16, 105.33
Int Tables number	1
Space group name H-M	P1

#1: Antibody	Human IgD Fab light chain Mass: 22769.070 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVitro / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody	Human IgD Fab heavy chain Mass: 25399.461 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.84 Å³/Da / Density % sol: 56.67 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350 and 0.2M sodium phosphate

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9179 Å
Detector	Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Nov 29, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9179 Å / Relative weight: 1
Reflection	Resolution: 2.75→69.15 Å / Num. obs: 27217 / % possible obs: 98.9 % / Redundancy: 3.5 % / B_iso Wilson estimate: 72.92 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.072 / R_pim(I) all: 0.046 / Net I/σ(I): 8.1
Reflection shell	Resolution: 2.75→2.88 Å / Redundancy: 3.2 % / R_merge(I) obs: 0.762 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3604 / CC_1/2: 0.776 / R_pim(I) all: 0.504 / % possible all: 98.5

-
Processing

Software

Name	Version	Classification
PHENIX	(1.19.2_4158: ???)	refinement
Aimless		data scaling
DIALS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.75→69.15 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 34.19 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2558	1415	5.21 %
R_work	0.2161	-	-
obs	0.2182	27159	98.71 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.75→69.15 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6567	0	9	13	6589

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	6774
X-RAY DIFFRACTION	f_angle_d	0.554	9260
X-RAY DIFFRACTION	f_dihedral_angle_d	11.949	2355
X-RAY DIFFRACTION	f_chiral_restr	0.043	1025
X-RAY DIFFRACTION	f_plane_restr	0.004	1192

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 (%)
2.75-2.85	0.4339	118	0.4417	2567	X-RAY DIFFRACTION	98
2.85-2.96	0.4147	152	0.3757	2533	X-RAY DIFFRACTION	98
2.96-3.1	0.3328	170	0.3209	2574	X-RAY DIFFRACTION	98
3.1-3.26	0.3575	135	0.3055	2565	X-RAY DIFFRACTION	99
3.26-3.46	0.3363	136	0.3037	2535	X-RAY DIFFRACTION	98
3.46-3.73	0.2921	137	0.2342	2580	X-RAY DIFFRACTION	99
3.73-4.11	0.264	137	0.2283	2600	X-RAY DIFFRACTION	99
4.11-4.7	0.229	105	0.1698	2635	X-RAY DIFFRACTION	99
4.7-5.92	0.184	144	0.1643	2589	X-RAY DIFFRACTION	100
5.92-69.15	0.22	181	0.1653	2566	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	1.0241	0.1394	0.3971	0.6788	-0.0937	2.3424	-0.2571	-0.1326	0.2747	0.0775	-0.2565	0.5814	-0.3368	-0.1616	-0.0066	0.8944	-0.1246	0.1985	0.7057	-0.0053	0.6881	-3.2782	-14.5547	48.001
2	0.1013	1.1406	1.0498	-0.1155	-1.1777	0.94	0.2926	0.155	-0.4477	-0.1144	-0.244	0.2025	-0.5342	-0.0079	0.0114	0.4579	-0.0783	-0.1079	0.5455	-0.0047	0.8334	-4.1326	-26.3637	28.1074
3	0.6348	-0.0223	-0.4085	3.0336	-0.6785	-0.2919	0.3074	0.1763	-0.0549	0.2758	-0.4124	1.6223	0.3413	0.1456	-0.0454	0.5178	-0.0499	-0.0615	0.5177	-0.0527	0.9333	-6.3903	-26.7106	20.4843
4	0.6894	0.9461	-0.3263	0.4928	0.167	0.1842	0.3721	-0.2088	-0.385	0.4407	-0.2241	0.2705	0.8954	0.1734	0.0229	1.5805	-0.2409	0.1175	0.8803	0.1285	0.7006	-0.0674	-37.7287	54.8902
5	0.4474	0.2942	0.0043	0.4827	0.2434	0.0698	0.8503	-0.3802	-0.0812	0.1614	-0.1968	0.5048	-0.2898	0.3465	0.0002	1.4256	-0.227	0.0473	1.1916	-0.0872	0.8902	-10.8091	-34.7457	54.3099
6	1.5332	-0.8102	0.6611	0.9904	0.0072	0.2906	-0.1738	-0.2367	-0.0859	0.8207	-0.0324	0.063	1.1073	-0.1848	-0.3672	1.3923	-0.2903	0.3393	0.7902	0.0543	0.583	-4.0103	-35.6798	53.8901
7	-0.3575	0.325	0.1997	0.1401	-0.0521	-0.0265	0.1511	0.2672	0.1043	0.3427	-0.5815	0.1447	-0.1607	0.5501	-0.0002	0.9246	0.0947	-0.2164	0.3604	0.0046	0.7209	1.9243	-43.7079	19.4275
8	0.5574	0.651	-0.4429	1.0608	1.164	0.2507	-0.286	0.1063	0.3495	0.1829	0.3705	-0.118	-0.2667	-0.1801	0.0001	0.7391	-0.0297	-0.2603	0.5925	0.0167	0.7915	7.5281	-33.425	12.3027
9	0.0223	-0.14	-0.154	-0.008	-0.2263	-0.1278	0.1484	0.325	0.0505	0.3864	-0.2056	-0.0894	-0.0827	0.4209	0.0006	0.7693	0.0497	-0.2319	0.4505	-0.0281	0.7308	1.6663	-37.6332	24.6581
10	0.0962	-0.0588	0.0092	-0.0582	0.0623	-0.0511	-0.8604	-1.3026	0.2264	-0.3095	0.4893	-1.0282	-0.2119	-0.0279	-0.0012	1.2401	-0.0781	-0.043	0.7958	0.1096	0.9344	8.166	-29.6214	1.9604
11	1.3614	-0.081	-1.2196	0.857	0.1563	0.4237	0.2739	0.1703	0.1414	-0.584	-0.1135	0.0059	0.6787	0.2515	0.7483	0.9528	0.0695	-0.4246	0.6004	-0.0503	0.9714	8.391	-41.6649	11.0321
12	0.1762	0.5732	0.2175	2.5778	0.7817	0.5648	-2.7615	0.695	1.4135	-2.6613	1.4349	-0.9468	-3.2424	0.61	-0.306	1.3102	0.0777	-0.3946	0.8965	0.0338	0.7746	-27.4109	8.866	-17.3961
13	0.682	-0.4178	0.463	2.286	0.5643	0.4288	-1.3721	-0.5973	0.2421	-0.6656	0.7126	0.6324	-1.3177	-0.4518	-0.0942	1.0645	0.005	-0.1712	1.0533	0.1047	0.6888	-33.5091	-1.7531	-18.4575
14	0.9781	0.2877	0.3707	0.7751	0.0923	1.0979	-0.8651	0.2616	0.7498	-1.0797	0.1858	0.1073	-1.0278	-0.9087	-0.6034	1.1186	0.2148	-0.0661	1.2383	-0.0261	0.4744	-28.3183	-0.17	-17.6606
15	0.3373	0.7037	-0.1568	0.9774	1.1652	0.9396	-0.0498	-0.4614	0.3659	-0.2852	-0.4624	-0.1328	0.4051	-0.4471	0.0039	0.7741	0.175	-0.1707	0.6346	-0.0701	0.7856	-9.8116	6.9981	9.6463
16	0.577	0.4959	-0.1586	0.619	-0.0683	0.0755	0.1204	0.148	-0.4717	-0.381	-0.575	-0.3829	-0.2627	0.0176	-0.0364	0.5562	0.1205	0.006	0.6585	-0.0277	0.5878	-3.7749	11.7479	7.5117
17	0.4779	0.19	0.0138	0.4757	0.215	0.7866	0.5441	-0.3038	0.034	-1.1113	-0.6403	0.2263	0.6596	-0.6	-0.2186	0.835	0.036	-0.0559	0.7187	-0.1334	0.7655	-12.1435	6.2562	5.5058
18	0.5187	0.6194	-0.2284	0.9032	-0.1196	0.6718	-0.9246	-0.1012	0.9398	0.5599	-0.0897	-1.3298	-1.2616	-0.0176	-0.0053	0.6861	0.0539	-0.3211	0.6619	-0.0168	0.8742	0.7531	13.8662	14.6113
19	1.1988	-0.2149	1.4147	5.8222	-1.1324	1.6667	0.5033	0.3033	-1.0512	-0.8323	0.7021	0.1187	0.8487	0.07	0.9799	-0.1762	-0.0383	0.4207	0.9822	-0.1479	0.5855	-19.7972	-17.0867	-11.5502
20	0.4883	0.521	-0.3039	0.2074	-0.3159	0.2224	0.388	-0.1426	0.1513	-0.3764	-0.444	0.1752	-0.9102	-0.3051	-0.0001	0.8109	0.1639	0.0137	0.6878	-0.0611	0.697	-7.6672	3.5883	21.4289
21	-0.4775	-0.5673	-0.2443	0.5118	0.0315	0.075	0.224	0.125	-0.3093	0.0029	-0.1443	0.3338	-0.1681	-0.0947	-0.071	0.5659	0.152	0.0863	0.6457	-0.0052	0.7334	-11.7062	-2.949	14.1372
22	0.6771	0.019	-0.4797	0.4204	-0.3967	0.5097	0.1267	0.3109	0.0622	0.3754	0.1628	0.057	0.4668	0.6431	-0.0005	0.6625	0.0119	-0.0147	0.5092	0.007	1.0411	-8.695	-9.1934	19.4883

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 94 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 95 through 134 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 135 through 216 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 2 through 40 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 41 through 64 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 65 through 119 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 120 through 134 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 135 through 174 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 175 through 191 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 192 through 202 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 203 through 225 )
12	X-RAY DIFFRACTION	12	chain 'L' and (resid 2 through 23 )
13	X-RAY DIFFRACTION	13	chain 'L' and (resid 24 through 71 )
14	X-RAY DIFFRACTION	14	chain 'L' and (resid 72 through 105 )
15	X-RAY DIFFRACTION	15	chain 'L' and (resid 106 through 134 )
16	X-RAY DIFFRACTION	16	chain 'L' and (resid 135 through 166 )
17	X-RAY DIFFRACTION	17	chain 'L' and (resid 167 through 185 )
18	X-RAY DIFFRACTION	18	chain 'L' and (resid 186 through 216 )
19	X-RAY DIFFRACTION	19	chain 'H' and (resid 2 through 134 )
20	X-RAY DIFFRACTION	20	chain 'H' and (resid 135 through 154 )
21	X-RAY DIFFRACTION	21	chain 'H' and (resid 155 through 202 )
22	X-RAY DIFFRACTION	22	chain 'H' and (resid 203 through 225 )

-
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