PDB-7prp: Crystal Structure of the B subunit of heat labile enterotoxin LT-...

ID or keywords:

Entry

Database: PDB / ID: 7prp

Title

Crystal Structure of the B subunit of heat labile enterotoxin LT-IIc from Escherichia coli in apo form

Components

Heat-labile enterotoxin IIA, B chain

Keywords

SUGAR BINDING PROTEIN / lectin / ganglioside / heat labile enterotoxin

Function / homology

Type II heat-labile enterotoxin, B subunit / Type II heat-labile enterotoxin, B subunit superfamily / Type II heat-labile enterotoxin , B subunit (LT-IIB) / Enterotoxin / extracellular region / FORMIC ACID / Heat-labile enterotoxin IIA, B chain

Function and homology information

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Varrot, A.

Funding support

European Union, 1items

Citation

Journal: Glycobiology / Year: 2022
Title: Characterization of the ganglioside recognition profile of Escherichia coli heat-labile enterotoxin LT-IIc.
Authors: Zalem, D. / Juhas, M. / Terrinoni, M. / King-Lyons, N. / Lebens, M. / Varrot, A. / Connell, T.D. / Teneberg, S.

History

Deposition	Sep 22, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 8, 2021	Provider: repository / Type: Initial release
Revision 1.1	Feb 2, 2022	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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	May 4, 2022	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3	Jan 31, 2024	Group: Data collection / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7prp.cif.gz	122.9 KB	Display	PDBx/mmCIF format
PDB format	pdb7prp.ent.gz		Display	PDB format
PDBx/mmJSON format	7prp.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pr/7prp ftp://data.pdbj.org/pub/pdb/validation_reports/pr/7prp	HTTPS FTP

-
Related structure data

Related structure data	7prsC 5g3lS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1po5-d 4nox-d 5a6r-d 3olb-4 3ol9-1 4k4z-4 5lzi-d 5wuf-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#69 - Sep 2005 Cholera Toxin similarity (1)

Deposited unit

DDD: Heat-labile enterotoxin IIA, B chain

EEE: Heat-labile enterotoxin IIA, B chain

FFF: Heat-labile enterotoxin IIA, B chain

GGG: Heat-labile enterotoxin IIA, B chain

HHH: Heat-labile enterotoxin IIA, B chain

hetero molecules

57.8 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	73.402, 73.688, 102.354
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: HIS / End label comp-ID: HIS / Auth seq-ID: 1 - 104 / Label seq-ID: 1 - 104

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20

#1: Protein	Heat-labile enterotoxin IIA, B chain / Heat-labile enterotoxin IIc B chain / Heat-labile enterotoxin type II B subunit Mass: 11499.999 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Details: Mature protein. numbering does not include peptide signal Source: (gene. exp.) Escherichia coli (E. coli) Gene: LT-IIc1 B, GQM13_12885, HVV37_03950, HVV78_10285, HVW37_13205 Plasmid: pBC1 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: H6W8F2
#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#3: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH₂O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.42 Å³/Da / Density % sol: 49.1 % / Description: needle
Crystal grow	Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 2.4 sodium formation and 100 mM citric acid pH 4.0.

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 9, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97857 Å / Relative weight: 1
Reflection	Resolution: 2.3→42 Å / Num. obs: 24817 / % possible obs: 99.6 % / Redundancy: 3.7 % / CC_1/2: 0.996 / R_merge(I) obs: 0.096 / R_pim(I) all: 0.079 / R_rim(I) all: 0.125 / Net I/σ(I): 8.1
Reflection shell	Resolution: 2.3→2.39 Å / Redundancy: 3.6 % / R_merge(I) obs: 0.455 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 9279 / CC_1/2: 0.806 / R_pim(I) all: 0.382 / R_rim(I) all: 0.597 / % possible all: 97.2

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
Aimless	0.5.032	data scaling
PHASER	2.8.2	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5G3L

5g3l

Resolution: 2.3→41.981 Å / Cor.coef. F_o:F_c: 0.945 / Cor.coef. F_o:F_c free: 0.913 / SU B: 7.87 / SU ML: 0.187 / Cross valid method: FREE R-VALUE / ESU R: 0.374 / ESU R Free: 0.246
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2448	1266	5.108 %
R_work	0.1958	23521	-
all	0.198	-	-
obs	-	24787	97.907 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 27.374 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.455 Å²	-0 Å²	-0 Å²
2-	-	-0.059 Å²	-0 Å²
3-	-	-	0.514 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→41.981 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4001	0	13	231	4245

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.013	4115
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	3700
X-RAY DIFFRACTION	r_angle_refined_deg	1.599	1.627	5608
X-RAY DIFFRACTION	r_angle_other_deg	1.381	1.577	8519
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.857	5	515
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.413	23.514	185
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.751	15	631
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	9.194	15	10
X-RAY DIFFRACTION	r_chiral_restr	0.075	0.2	550
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	4741
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	927
X-RAY DIFFRACTION	r_nbd_refined	0.21	0.2	678
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.181	0.2	3271
X-RAY DIFFRACTION	r_nbtor_refined	0.159	0.2	1921
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.08	0.2	1972
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.196	0.2	115
X-RAY DIFFRACTION	r_metal_ion_refined	0.175	0.2	14
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.117	0.2	20
X-RAY DIFFRACTION	r_nbd_other	0.191	0.2	67
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.165	0.2	9
X-RAY DIFFRACTION	r_mcbond_it	2.796	2.659	2075
X-RAY DIFFRACTION	r_mcbond_other	2.796	2.658	2074
X-RAY DIFFRACTION	r_mcangle_it	4.026	3.981	2585
X-RAY DIFFRACTION	r_mcangle_other	4.025	3.982	2586
X-RAY DIFFRACTION	r_scbond_it	4.222	3.254	2040
X-RAY DIFFRACTION	r_scbond_other	4.224	3.256	2040
X-RAY DIFFRACTION	r_scangle_it	6.358	4.658	3023
X-RAY DIFFRACTION	r_scangle_other	6.358	4.66	3023
X-RAY DIFFRACTION	r_lrange_it	8.04	31.571	4321
X-RAY DIFFRACTION	r_lrange_other	8.01	31.513	4304
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.089	0.05	3059
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.081	0.05	3071
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.065	0.05	3096
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.08	0.05	3070
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.089	0.05	3090
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.09	0.05	3072
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.092	0.05	3075
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.08	0.05	3091
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.082	0.05	3089
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.074	0.05	3117

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	DDD	X-RAY DIFFRACTION	Local ncs	0.08884	0.05009
1	2	EEE	X-RAY DIFFRACTION	Local ncs	0.08884	0.05009
2	3	DDD	X-RAY DIFFRACTION	Local ncs	0.08132	0.05009
2	4	FFF	X-RAY DIFFRACTION	Local ncs	0.08132	0.05009
3	5	DDD	X-RAY DIFFRACTION	Local ncs	0.06525	0.05009
3	6	GGG	X-RAY DIFFRACTION	Local ncs	0.06525	0.05009
4	7	DDD	X-RAY DIFFRACTION	Local ncs	0.08015	0.05009
4	8	HHH	X-RAY DIFFRACTION	Local ncs	0.08015	0.05009
5	9	EEE	X-RAY DIFFRACTION	Local ncs	0.0893	0.05009
5	10	FFF	X-RAY DIFFRACTION	Local ncs	0.0893	0.05009
6	11	EEE	X-RAY DIFFRACTION	Local ncs	0.09014	0.05009
6	12	GGG	X-RAY DIFFRACTION	Local ncs	0.09014	0.05009
7	13	EEE	X-RAY DIFFRACTION	Local ncs	0.09221	0.05009
7	14	HHH	X-RAY DIFFRACTION	Local ncs	0.09221	0.05009
8	15	FFF	X-RAY DIFFRACTION	Local ncs	0.07989	0.05009
8	16	GGG	X-RAY DIFFRACTION	Local ncs	0.07989	0.05009
9	17	FFF	X-RAY DIFFRACTION	Local ncs	0.08175	0.05009
9	18	HHH	X-RAY DIFFRACTION	Local ncs	0.08175	0.05009
10	19	GGG	X-RAY DIFFRACTION	Local ncs	0.07446	0.05009
10	20	HHH	X-RAY DIFFRACTION	Local ncs	0.07446	0.05009

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 (%)
2.3-2.36	0.307	88	0.245	1677	X-RAY DIFFRACTION	96.0806
2.36-2.424	0.27	95	0.246	1696	X-RAY DIFFRACTION	99.2244
2.424-2.494	0.335	79	0.238	1634	X-RAY DIFFRACTION	99.4196
2.494-2.571	0.26	71	0.233	1606	X-RAY DIFFRACTION	99.1721
2.571-2.655	0.324	99	0.226	1540	X-RAY DIFFRACTION	99.0931
2.655-2.747	0.243	68	0.2	1504	X-RAY DIFFRACTION	99.0548
2.747-2.851	0.225	81	0.191	1430	X-RAY DIFFRACTION	97.9896
2.851-2.966	0.227	65	0.185	1359	X-RAY DIFFRACTION	96.9367
2.966-3.098	0.259	75	0.209	1358	X-RAY DIFFRACTION	99.0325
3.098-3.248	0.276	79	0.201	1268	X-RAY DIFFRACTION	99.0441
3.248-3.422	0.197	64	0.184	1217	X-RAY DIFFRACTION	98.4627
3.422-3.629	0.196	67	0.164	1155	X-RAY DIFFRACTION	98.7076
3.629-3.877	0.246	47	0.171	1071	X-RAY DIFFRACTION	95.5556
3.877-4.185	0.225	68	0.152	997	X-RAY DIFFRACTION	97.7961
4.185-4.58	0.191	65	0.139	932	X-RAY DIFFRACTION	97.7451
4.58-5.113	0.216	43	0.153	833	X-RAY DIFFRACTION	95.9474
5.113-5.889	0.23	33	0.21	768	X-RAY DIFFRACTION	96.8561
5.889-7.177	0.349	31	0.279	651	X-RAY DIFFRACTION	95.6522
7.177-10	0.272	32	0.233	507	X-RAY DIFFRACTION	95.7371

-
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