PDB-6b0w: Crystal structure of the anti-circumsporozoite protein 1710 antibody

ID or keywords:

Entry

Database: PDB / ID: 6b0w

Title

Crystal structure of the anti-circumsporozoite protein 1710 antibody

Components

1710 antibody, heavy chain
1710 antibody, light chain

Keywords

IMMUNE SYSTEM /

Malaria /

Circumsporozoite protein / alpha thrombospondin type-1 repeat

Function / homology

Immunoglobulins /

Immunoglobulin-like /

Sandwich / Mainly Beta /

ISOPROPYL ALCOHOL

Function and homology information

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Scally, S.W. / Murugan, R. / Bosch, A. / Triller, G. / Wardemann, H. / Julien, J.P.

Citation

Journal: J. Exp. Med. / Year: 2018
Title: Rare PfCSP C-terminal antibodies induced by live sporozoite vaccination are ineffective against malaria infection.
Authors: Scally, S.W. / Murugan, R. / Bosch, A. / Triller, G. / Costa, G. / Mordmuller, B. / Kremsner, P.G. / Sim, B.K.L. / Hoffman, S.L. / Levashina, E.A. / Wardemann, H. / Julien, J.P.

History

Deposition	Sep 15, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 8, 2017	Provider: repository / Type: Initial release
Revision 1.1	Dec 6, 2017	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Jan 10, 2018	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3	Oct 4, 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

-
Download

PDBx/mmCIF format	6b0w.cif.gz	185.6 KB	Display	PDBx/mmCIF format
PDB format	pdb6b0w.ent.gz	145.2 KB	Display	PDB format
PDBx/mmJSON format	6b0w.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b0/6b0w ftp://data.pdbj.org/pub/pdb/validation_reports/b0/6b0w	HTTPS FTP

-
Related structure data

Related structure data	6b0sC 4gsdS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4hpy-d 1i7z-1 6ev2-3 4hs6-2 4x7t-1 6wfy-d 1zan-d 6bb4-3 5ig7-4 5ubz-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	#256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #21 - Sep 2001 Antibodies similarity (1) #70 - Oct 2005 Designer Proteins similarity (1)

Deposited unit

L: 1710 antibody, light chain

H: 1710 antibody, heavy chain

hetero molecules

47.5 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)	61.063, 66.724, 124.027
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Antibody	1710 antibody, light chain Mass: 22629.990 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody	1710 antibody, heavy chain Mass: 23940.674 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Chemical	ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol Mass: 60.095 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃H₈O / Comment: alkaloid*YM
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.71 Å³/Da / Density % sol: 54.66 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 17 % (w/v) PEG 400, 15 % (v/v) glycerol, 8.5 % (v/v) isopropanol and 85 mM HEPES pH 7.5

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
Detector	Type: RAYONIX MX300HE / Detector: CCD / Date: Mar 16, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97949 Å / Relative weight: 1
Reflection	Resolution: 1.9→45.424 Å / Num. obs: 40776 / % possible obs: 99.5 % / Redundancy: 5.4 % / R_pim(I) all: 0.044 / Net I/σ(I): 13.2
Reflection shell	Resolution: 1.9→2 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 5691 / R_pim(I) all: 0.289 / % possible all: 99.2

-
Processing

Software

Name	Version	Classification
PHENIX	(1.12_2829: ???)	refinement
XDS		data reduction
XPREP		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4GSD

4gsd

Resolution: 1.9→45.424 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.5

	R_factor	Num. reflection	% reflection
R_free	0.2179	2000	4.94 %
R_work	0.1833	-	-
obs	0.185	40542	99.61 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.9→45.424 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3224	0	60	240	3524

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	3382
X-RAY DIFFRACTION	f_angle_d	0.787	4612
X-RAY DIFFRACTION	f_dihedral_angle_d	13.774	2013
X-RAY DIFFRACTION	f_chiral_restr	0.053	517
X-RAY DIFFRACTION	f_plane_restr	0.005	585

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 (%)
1.9-1.9241	0.3082	134	0.311	2710	X-RAY DIFFRACTION	99
1.9241-1.9494	0.328	133	0.2971	2663	X-RAY DIFFRACTION	100
1.9494-1.9761	0.3355	141	0.2812	2723	X-RAY DIFFRACTION	99
1.9761-2.0043	0.3077	144	0.2714	2688	X-RAY DIFFRACTION	100
2.0043-2.0342	0.3087	142	0.2583	2695	X-RAY DIFFRACTION	99
2.0342-2.066	0.2925	141	0.2448	2709	X-RAY DIFFRACTION	100
2.066-2.0999	0.2691	141	0.2354	2716	X-RAY DIFFRACTION	99
2.0999-2.1361	0.2897	139	0.2236	2689	X-RAY DIFFRACTION	100
2.1361-2.175	0.2307	143	0.2141	2695	X-RAY DIFFRACTION	99
2.175-2.2168	0.2565	138	0.2191	2710	X-RAY DIFFRACTION	100
2.2168-2.262	0.2281	139	0.207	2726	X-RAY DIFFRACTION	100
2.262-2.3112	0.2743	139	0.2128	2694	X-RAY DIFFRACTION	100
2.3112-2.365	0.2464	142	0.2146	2705	X-RAY DIFFRACTION	100
2.365-2.4241	0.2688	135	0.207	2688	X-RAY DIFFRACTION	100
2.4241-2.4897	0.2327	143	0.2033	2720	X-RAY DIFFRACTION	100
2.4897-2.5629	0.2319	143	0.1954	2741	X-RAY DIFFRACTION	100
2.5629-2.6456	0.2433	134	0.1937	2693	X-RAY DIFFRACTION	100
2.6456-2.7402	0.2474	145	0.1901	2710	X-RAY DIFFRACTION	100
2.7402-2.8499	0.2266	140	0.1731	2691	X-RAY DIFFRACTION	100
2.8499-2.9796	0.2025	138	0.1662	2689	X-RAY DIFFRACTION	100
2.9796-3.1366	0.1922	147	0.1597	2732	X-RAY DIFFRACTION	100
3.1366-3.3331	0.1705	143	0.1609	2717	X-RAY DIFFRACTION	100
3.3331-3.5903	0.1685	145	0.1451	2693	X-RAY DIFFRACTION	100
3.5903-3.9514	0.2261	140	0.1618	2716	X-RAY DIFFRACTION	100
3.9514-4.5228	0.1863	142	0.1454	2697	X-RAY DIFFRACTION	100
4.5228-5.6965	0.1884	139	0.1596	2707	X-RAY DIFFRACTION	100
5.6965-45.4372	0.1969	146	0.1908	2718	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	3.5549	0.7717	0.0124	2.2626	0.7612	4.5753	-0.0364	-0.0771	-0.2221	0.2047	0.0468	-0.0159	0.1234	0.1563	0.0095	0.2118	0.0363	0.04	0.1962	0.0189	0.1954	-3.6879	-22.5867	9.3314
2	1.9192	-0.5672	-1.0599	0.6565	0.5326	0.6321	0.0137	-0.0352	-0.0392	-0.0059	-0.0376	-0.01	-0.0659	0.0297	0.0034	0.2238	-0.0161	-0.0231	0.1412	0.0092	0.1525	-23.5318	-12.4334	22.3562
3	7.3868	-4.6026	3.0131	5.6015	-2.8101	3.4116	0.1261	0.0267	-0.194	-0.2712	-0.1066	0.3634	0.045	-0.2002	0.0174	0.2208	-0.0191	0.011	0.1904	-0.0338	0.1225	-33.5449	-11.5149	20.93
4	4.9056	-0.4678	-2.4081	1.9232	0.8524	4.1113	0.1365	0.144	0.4761	0.02	0.1015	0.0311	-0.4304	-0.1291	-0.2268	0.2886	0.0326	0.0262	0.1719	0.0428	0.2085	-1.876	-0.6601	3.3107
5	5.5505	-1.826	-2.0545	4.6246	-0.7968	4.2208	0.0839	0.0561	0.3467	-0.0039	0.1161	0.0872	-0.1501	-0.0992	-0.1968	0.2327	0.0026	-0.0214	0.1897	0.0066	0.1708	-1.3254	-1.5847	3.9436
6	5.5537	-0.2186	-0.6405	3.8918	-0.0091	5.6263	0.0689	0.0465	0.0172	-0.2888	0.0617	-0.2799	0.8116	-0.1051	-0.1936	0.354	0.0217	-0.0096	0.1546	-0.0377	0.1871	-27.3688	-1.057	33.56
7	3.9023	-0.2806	-1.0914	4.7263	0.7053	4.4773	0.0735	-0.382	0.042	0.4255	0.0912	-0.0327	0.3992	-0.0046	-0.173	0.3222	0.0054	-0.0219	0.1895	-0.0225	0.167	-27.9643	-1.621	37.5089

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'L' and (resid 2 through 92 )
2	X-RAY DIFFRACTION	2	chain 'L' and (resid 93 through 172 )
3	X-RAY DIFFRACTION	3	chain 'L' and (resid 173 through 211 )
4	X-RAY DIFFRACTION	4	chain 'H' and (resid 1 through 66 )
5	X-RAY DIFFRACTION	5	chain 'H' and (resid 67 through 111 )
6	X-RAY DIFFRACTION	6	chain 'H' and (resid 112 through 157 )
7	X-RAY DIFFRACTION	7	chain 'H' and (resid 158 through 214 )

-
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