PDB-5i66: X-ray structure of the Fab fragment of 8B6, a murine monoclonal a...

ID or keywords:

Entry

Database: PDB / ID: 5i66

Title

X-ray structure of the Fab fragment of 8B6, a murine monoclonal antibody specific for the human serotonin transporter

Components

8B6 antibody, heavy chain
8B6 antibody, light chain

Keywords

IMMUNE SYSTEM / Immunoglobulin fold

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta

Function and homology information

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.624 Å

Authors

Coleman, J.A. / Green, E.M. / Gouaux, E.

Funding support

United States, 2items

Citation

Journal: Nature / Year: 2016
Title: X-ray structures and mechanism of the human serotonin transporter.
Authors: Coleman, J.A. / Green, E.M. / Gouaux, E.

History

Deposition	Feb 16, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 13, 2016	Provider: repository / Type: Initial release
Revision 1.1	Apr 20, 2016	Group: Database references
Revision 1.2	May 4, 2016	Group: Database references
Revision 1.3	Nov 20, 2019	Group: Author supporting evidence / Database references / Derived calculations Category: citation / pdbx_audit_support / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4	Sep 27, 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 1.5	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5i66.cif.gz	254.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5i66.ent.gz	208.5 KB	Display	PDB format
PDBx/mmJSON format	5i66.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5i66_validation.pdf.gz	431 KB	Display	wwPDB validaton report
Full document	5i66_full_validation.pdf.gz	433.9 KB	Display
Data in XML	5i66_validation.xml.gz	20 KB	Display
Data in CIF	5i66_validation.cif.gz	29.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/i6/5i66 ftp://data.pdbj.org/pub/pdb/validation_reports/i6/5i66	HTTPS FTP

-
Related structure data

Related structure data	5i6xC 5i6zC 5i71C 5i73C 5i74C 5i75C 4lqfS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5i8o-d 7jwq-2 5mv3-6 1mre-d 5i1i-d 2xa8-d 3qct-d 1t4k-1 6xul-3 4x7t-2 1rum-d 4x80-d 1qyg-d 5b3j-3 1s5i-d 3o6k-d 5mub-1 1ruk-d 5dub-2 2adj-d Search similar-shape structures by Omokage search (details) 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: 8B6 antibody, heavy chain

B: 8B6 antibody, light chain

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	81.560, 81.560, 142.170
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

#1: Antibody	8B6 antibody, heavy chain Mass: 23688.365 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm)
#2: Antibody	8B6 antibody, light chain Mass: 23718.217 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm)
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.29 Å³/Da / Density % sol: 46.19 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 100 mM HEPES pH 7.5, 300 mM NH4H2PO4 and 22.5% pure PEG (0.3-0.8 kDa)

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 18, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.62→57.672 Å / Num. obs: 117803 / % possible obs: 97.7 % / Redundancy: 6.7 % / R_merge(I) obs: 0.0522 / Net I/σ(I): 18.9

-
Processing

Software

Name	Version	Classification
PHENIX	(1.10_2142: ???)	refinement
XDS		data reduction
PHASER		phasing
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4LQF

4lqf

Resolution: 1.624→57.672 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.12 / Phase error: 22.92

	R_factor	Num. reflection	% reflection
R_free	0.198	5637	5.03 %
R_work	0.1782	-	-
obs	0.1792	112166	96.96 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.624→57.672 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3302	0	0	302	3604

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	3389
X-RAY DIFFRACTION	f_angle_d	1.148	4620
X-RAY DIFFRACTION	f_dihedral_angle_d	12.996	2018
X-RAY DIFFRACTION	f_chiral_restr	0.057	520
X-RAY DIFFRACTION	f_plane_restr	0.007	584

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 (%)
1.6237-1.6421	0.3719	76	0.4331	1383	X-RAY DIFFRACTION	38
1.6421-1.6614	0.3843	165	0.3809	2974	X-RAY DIFFRACTION	81
1.6614-1.6817	0.3897	177	0.3423	3310	X-RAY DIFFRACTION	91
1.6817-1.703	0.3599	191	0.3129	3665	X-RAY DIFFRACTION	100
1.703-1.7254	0.3141	194	0.2972	3678	X-RAY DIFFRACTION	100
1.7254-1.749	0.3118	194	0.2897	3642	X-RAY DIFFRACTION	100
1.749-1.774	0.3229	196	0.2854	3688	X-RAY DIFFRACTION	100
1.774-1.8005	0.3205	185	0.2676	3625	X-RAY DIFFRACTION	100
1.8005-1.8287	0.2814	192	0.2485	3671	X-RAY DIFFRACTION	100
1.8287-1.8586	0.2945	197	0.2371	3656	X-RAY DIFFRACTION	100
1.8586-1.8907	0.2379	191	0.225	3682	X-RAY DIFFRACTION	100
1.8907-1.9251	0.2574	191	0.2089	3675	X-RAY DIFFRACTION	100
1.9251-1.9621	0.2078	191	0.1891	3632	X-RAY DIFFRACTION	100
1.9621-2.0021	0.2225	195	0.1957	3664	X-RAY DIFFRACTION	100
2.0021-2.0457	0.2394	195	0.1826	3688	X-RAY DIFFRACTION	100
2.0457-2.0933	0.24	195	0.1761	3646	X-RAY DIFFRACTION	100
2.0933-2.1456	0.2097	192	0.1679	3683	X-RAY DIFFRACTION	100
2.1456-2.2036	0.1949	195	0.1672	3646	X-RAY DIFFRACTION	100
2.2036-2.2685	0.2156	190	0.1716	3663	X-RAY DIFFRACTION	100
2.2685-2.3417	0.1922	194	0.1758	3675	X-RAY DIFFRACTION	100
2.3417-2.4254	0.2063	189	0.1737	3609	X-RAY DIFFRACTION	100
2.4254-2.5225	0.2144	198	0.1746	3689	X-RAY DIFFRACTION	100
2.5225-2.6373	0.2347	198	0.1775	3683	X-RAY DIFFRACTION	100
2.6373-2.7764	0.1752	188	0.1738	3655	X-RAY DIFFRACTION	100
2.7764-2.9503	0.2051	193	0.1735	3665	X-RAY DIFFRACTION	100
2.9503-3.1781	0.1861	193	0.1764	3639	X-RAY DIFFRACTION	100
3.1781-3.4979	0.1983	198	0.1762	3681	X-RAY DIFFRACTION	100
3.4979-4.0039	0.178	194	0.1542	3649	X-RAY DIFFRACTION	100
4.0039-5.044	0.1313	198	0.1315	3653	X-RAY DIFFRACTION	100
5.044-57.708	0.1693	192	0.1781	3660	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	1.5696	-0.7576	-0.6581	3.2654	1.0837	1.8601	0.0958	0.1666	0.3314	0.0802	-0.0691	-0.2101	-0.1809	-0.0493	0.0058	0.2287	0.0329	0.0073	0.2313	0.0908	0.2883	64.5247	85.8935	66.3587
2	7.1916	1.4284	-1.8045	2.0546	-0.4738	2.6238	-0.1876	0.5751	0.3847	-0.1053	0.2026	0.5874	0.1278	-0.4037	0.0229	0.2725	-0.0279	0.0138	0.3456	0.0421	0.3528	39.5808	68.2307	57.1696
3	4.6212	-0.7155	-0.683	1.8863	0.3726	1.7761	-0.2172	-0.3306	0.2662	0.3952	0.1483	-0.1012	0.0228	-0.0168	0.0616	0.326	0.0573	0.0115	0.1793	0.0112	0.1763	55.8284	80.8354	85.3293
4	1.5633	0.0134	0.6344	1.727	1.1705	4.0574	-0.1626	0.1991	-0.4473	0.0943	0.0393	0.3918	0.6202	0.0986	0.0413	0.4889	-0.0391	0.1336	0.2747	-0.056	0.4198	38.5039	54.9747	65.273

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 21:138)
2	X-RAY DIFFRACTION	2	(chain A and resid 139:237)
3	X-RAY DIFFRACTION	3	(chain B and resid 22:124)
4	X-RAY DIFFRACTION	4	(chain B and resid 125:233)

-
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