PDB-9i7z: LecA in complex with 2-fluoro non-carbohydrate glycomimetic

ID or keywords:

Entry

Database: PDB / ID: 9i7z

Title

LecA in complex with 2-fluoro non-carbohydrate glycomimetic

Components

PA-I galactophilic lectin

Keywords

SUGAR BINDING PROTEIN / drug repurposing / glycomimetics / catechols / lectins / inhibitors

Function / homology

Function and homology information

heterophilic cell-cell adhesion / carbohydrate binding / periplasmic space / cell surface / cytoplasm
Similarity search - Function

Biological species

Pseudomonas aeruginosa PAO1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.85 Å

Authors

Varrot, A.

Funding support

France,

Germany, 2items

Citation

Journal: Angew.Chem.Int.Ed.Engl. / Year: 2025
Title: The Parkinson's Disease Drug Tolcapone and Analogues are Potent Glycomimetic Lectin Inhibitors of Pseudomonas aeruginosa LecA
Authors: Leusmann, S. / Siebs, E. / Varrot, A. / Kuhaudomlarp, S. / Imberty, A. / Kuhn, B. / Lerner, C. / Grether, U. / Titz, A.

History

Deposition	Feb 3, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 22, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9i7z.cif.gz	124.5 KB	Display	PDBx/mmCIF format
PDB format	pdb9i7z.ent.gz		Display	PDB format
PDBx/mmJSON format	9i7z.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	9i7z_validation.pdf.gz	3.9 MB	Display	wwPDB validaton report
Full document	9i7z_full_validation.pdf.gz	3.9 MB	Display
Data in XML	9i7z_validation.xml.gz	28.7 KB	Display
Data in CIF	9i7z_validation.cif.gz	39.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/i7/9i7z ftp://data.pdbj.org/pub/pdb/validation_reports/i7/9i7z	HTTPS FTP

-
Related structure data

Related structure data	9i80C 8guv C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Experimental dataset #1	Data reference: 10.5281/zenodo.14843851 / Data set type: diffraction image data

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: PA-I galactophilic lectin

B: PA-I galactophilic lectin

C: PA-I galactophilic lectin

D: PA-I galactophilic lectin

hetero molecules

53.8 kDa, 4 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)	60.576, 50.728, 71.689
Angle α, β, γ (deg.)	90.000, 100.011, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	2	A
4	2	C
5	3	A
6	3	D
7	4	B
8	4	C
9	5	B
10	5	D
11	6	C
12	6	D

NCS domain segments:

Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: SER / End label comp-ID: SER / Auth seq-ID: 1 - 121 / Label seq-ID: 1 - 121

Dom-ID	Component-ID	Ens-ID	Auth asym-ID	Label asym-ID
1	1	1	A	A
2	1	1	B	B
3	2	2	A	A
4	2	2	C	C
5	3	3	A	A
6	3	3	D	D
7	4	4	B	B
8	4	4	C	C
9	5	5	B	B
10	5	5	D	D
11	6	6	C	C
12	6	6	D	D

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

-
Protein , 1 types, 4 molecules ABCD

#1: Protein	PA-I galactophilic lectin / PA-IL / Galactose-binding lectin Mass: 12770.137 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: N terminal methionine cleaved / Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: lecA, pa1L, PA2570 / Plasmid: LecA-pet25b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q05097

#1: Protein

PA-I galactophilic lectin / PA-IL / Galactose-binding lectin

Mass: 12770.137 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: N terminal methionine cleaved / Source: (gene. exp.)

Pseudomonas aeruginosa PAO1 (bacteria) / Gene: lecA, pa1L, PA2570 / Plasmid: LecA-pet25b / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q05097

-
Non-polymers , 10 types, 409 molecules

#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-A1IZM / [2,6-bis(fluoranyl)phenyl]-[3-nitro-4,5-bis(oxidanyl)phenyl]methanone Mass: 295.195 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₃H₇F₂NO₅ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₂₂O₆ / Comment: precipitant*YM
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#7: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#8: Chemical	ChemComp-9YU / 2-[2-[2-[2-[2-[2-(2-methoxyethoxy)ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethanol Mass: 340.410 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₅H₃₂O₈
#9: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#10: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#11: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 389 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	Y
Has protein modification	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.01 Å³/Da / Density % sol: 38.83 % / Description: plate
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 26% Peg 6K, 1M LiCl and 100 mM sodium acetate pH 4.5

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 22, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9786 Å / Relative weight: 1
Reflection	Resolution: 1.85→42.1 Å / Num. obs: 36840 / % possible obs: 99.9 % / Redundancy: 5.5 % / B_iso Wilson estimate: 20.3 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.08 / R_pim(I) all: 0.057 / R_rim(I) all: 0.098 / Net I/σ(I): 12.4
Reflection shell	Resolution: 1.85→1.89 Å / Redundancy: 5.2 % / R_merge(I) obs: 0.563 / Num. unique obs: 2274 / CC_1/2: 0.814 / R_pim(I) all: 0.42 / R_rim(I) all: 0.706 / % possible all: 100

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0430	refinement
XDS		data reduction
Aimless		data scaling
PHASER	2.8.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.85→41.23 Å / Cor.coef. F_o:F_c: 0.969 / Cor.coef. F_o:F_c free: 0.946 / SU B: 3.51 / SU ML: 0.103 / Cross valid method: FREE R-VALUE / ESU R: 0.142 / ESU R Free: 0.133
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2042	1850	5.023 %
R_work	0.1581	34977	-
all	0.161	-	-
obs	-	36827	99.916 %

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: 24.2 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.217 Å²	-0 Å²	1.719 Å²
2-	-	0.085 Å²	-0 Å²
3-	-	-	-1.797 Å²

Refinement step

Cycle: LAST / Resolution: 1.85→41.23 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3593	0	173	389	4155

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.012	3845
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	3473
X-RAY DIFFRACTION	r_angle_refined_deg	1.821	1.743	5233
X-RAY DIFFRACTION	r_angle_other_deg	0.637	1.726	7980
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.705	5	478
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	44.222	16.25	32
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.775	10	514
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.211	10	162
X-RAY DIFFRACTION	r_chiral_restr	0.102	0.2	543
X-RAY DIFFRACTION	r_gen_planes_refined	0.013	0.02	4646
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	878
X-RAY DIFFRACTION	r_nbd_refined	0.202	0.2	668
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.203	0.2	3164
X-RAY DIFFRACTION	r_nbtor_refined	0.184	0.2	1956
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.093	0.2	2030
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.143	0.2	287
X-RAY DIFFRACTION	r_metal_ion_refined	0.112	0.2	19
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.232	0.2	11
X-RAY DIFFRACTION	r_nbd_other	0.157	0.2	39
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.11	0.2	13
X-RAY DIFFRACTION	r_mcbond_it	3.174	2.436	1928
X-RAY DIFFRACTION	r_mcbond_other	3.174	2.435	1928
X-RAY DIFFRACTION	r_mcangle_it	3.823	4.343	2400
X-RAY DIFFRACTION	r_mcangle_other	3.823	4.343	2401
X-RAY DIFFRACTION	r_scbond_it	4.156	2.798	1917
X-RAY DIFFRACTION	r_scbond_other	4.155	2.798	1918
X-RAY DIFFRACTION	r_scangle_it	5.797	4.959	2833
X-RAY DIFFRACTION	r_scangle_other	5.796	4.959	2834
X-RAY DIFFRACTION	r_lrange_it	6.602	25.862	4408
X-RAY DIFFRACTION	r_lrange_other	6.565	24.82	4343
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.109	0.05	3554
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.093	0.05	3628
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.124	0.05	3556
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.098	0.05	3567
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.111	0.05	3531
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.12	0.05	3561

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.10905	0.05008
1	2	B	X-RAY DIFFRACTION	Local ncs	0.10905	0.05008
2	3	A	X-RAY DIFFRACTION	Local ncs	0.09329	0.05008
2	4	C	X-RAY DIFFRACTION	Local ncs	0.09329	0.05008
3	5	A	X-RAY DIFFRACTION	Local ncs	0.1242	0.05008
3	6	D	X-RAY DIFFRACTION	Local ncs	0.1242	0.05008
4	7	B	X-RAY DIFFRACTION	Local ncs	0.09757	0.05009
4	8	C	X-RAY DIFFRACTION	Local ncs	0.09757	0.05009
5	9	B	X-RAY DIFFRACTION	Local ncs	0.11124	0.05008
5	10	D	X-RAY DIFFRACTION	Local ncs	0.11124	0.05008
6	11	C	X-RAY DIFFRACTION	Local ncs	0.12033	0.05008
6	12	D	X-RAY DIFFRACTION	Local ncs	0.12033	0.05008

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.85-1.898	0.259	136	0.23	2554	0.231	2690	0.955	0.957	100	0.206
1.898-1.95	0.235	136	0.205	2524	0.207	2664	0.96	0.965	99.8499	0.18
1.95-2.006	0.24	120	0.188	2406	0.191	2528	0.962	0.972	99.9209	0.165
2.006-2.068	0.228	133	0.181	2353	0.184	2487	0.961	0.976	99.9598	0.159
2.068-2.136	0.217	100	0.164	2318	0.166	2424	0.969	0.981	99.7525	0.142
2.136-2.21	0.216	118	0.151	2235	0.154	2353	0.97	0.985	100	0.13
2.21-2.293	0.227	120	0.158	2107	0.162	2230	0.968	0.985	99.8655	0.139
2.293-2.387	0.217	96	0.154	2089	0.157	2187	0.969	0.985	99.9085	0.136
2.387-2.493	0.179	96	0.147	1987	0.148	2083	0.979	0.986	100	0.131
2.493-2.614	0.25	90	0.148	1908	0.152	1998	0.962	0.986	100	0.134
2.614-2.754	0.21	125	0.15	1806	0.154	1931	0.972	0.986	100	0.138
2.754-2.921	0.239	97	0.163	1675	0.167	1773	0.966	0.983	99.9436	0.152
2.921-3.121	0.22	106	0.168	1585	0.171	1691	0.968	0.983	100	0.16
3.121-3.37	0.202	74	0.156	1516	0.158	1590	0.977	0.986	100	0.153
3.37-3.689	0.16	67	0.144	1383	0.145	1451	0.983	0.989	99.9311	0.144
3.689-4.12	0.186	78	0.134	1250	0.137	1328	0.98	0.99	100	0.136
4.12-4.75	0.148	50	0.117	1129	0.118	1179	0.991	0.992	100	0.124
4.75-5.798	0.178	49	0.149	951	0.15	1001	0.988	0.989	99.9001	0.156
5.798-8.12	0.184	37	0.186	754	0.186	793	0.977	0.983	99.7478	0.191
8.12-41.23	0.206	22	0.204	447	0.204	473	0.979	0.978	99.1543	0.231

-
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

-
Protein , 1 types, 4 molecules ABCD

-
Non-polymers , 10 types, 409 molecules

-
Details

-
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

-Protein , 1 types, 4 molecules ABCD

-Non-polymers , 10 types, 409 molecules

-Details

-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

-
Protein , 1 types, 4 molecules ABCD

-
Non-polymers , 10 types, 409 molecules

-
Details

-
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