PDB-9hd4: LecB in complex with photoswitchable compound GTB

ID or keywords:

Entry

Database: PDB / ID: 9hd4

Title

LecB in complex with photoswitchable compound GTB

Components

Fucose-binding lectin PA-IIL

Keywords

SUGAR BINDING PROTEIN / LECTIN / CELL ADHESION / PHOTOSWITCHABLE LIGAND

Function / homology

Calcium-mediated lectin / Calcium-mediated lectin superfamily / Fucose-binding lectin II (PA-IIL) / carbohydrate binding / metal ion binding / : / Fucose-binding lectin PA-IIL

Function and homology information

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.491 Å

Authors

Parisini, E. / Bhattacharya, S.

Funding support

European Union, 1items

Citation

Journal: To Be Published
Title: Crystal structure of Pseudomonas aeruginosa LecB in complex with photoswitchable compound GTB
Authors: Bhattacharya, S. / Parisini, E.

History

Deposition	Nov 11, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 19, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9hd4.cif.gz	470.8 KB	Display	PDBx/mmCIF format
PDB format	pdb9hd4.ent.gz		Display	PDB format
PDBx/mmJSON format	9hd4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hd/9hd4 ftp://data.pdbj.org/pub/pdb/validation_reports/hd/9hd4	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Fucose-binding lectin PA-IIL

B: Fucose-binding lectin PA-IIL

C: Fucose-binding lectin PA-IIL

D: Fucose-binding lectin PA-IIL

hetero molecules

48.8 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)	64.210, 83.720, 158.880
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

#1: Protein	Fucose-binding lectin PA-IIL Mass: 11676.710 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: lecB, PA14_20610 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2ZE85
#2: Chemical	ChemComp-A1IT5 / ~{N}-[[(2~{R},3~{S},4~{R},5~{S},6~{S})-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl]methyl]-4-[(~{Z})-phenyldiazenyl]benzenesulfonamide Mass: 421.467 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₉H₂₃N₃O₆S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 398 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.29 Å³/Da / Density % sol: 46.19 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.3 / Details: 20% PEG 8K, 0.25M LiCl, 0.1M Sodium acetate pH 4.3

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 15, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9537 Å / Relative weight: 1
Reflection	Resolution: 1.491→79.44 Å / Num. obs: 69682 / % possible obs: 99.4 % / Redundancy: 12.4 % / CC_1/2: 0.994 / Net I/σ(I): 8
Reflection shell	Resolution: 1.491→1.516 Å / Num. unique obs: 3457 / CC_1/2: 0.319

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0352	refinement
autoPROC		data reduction
autoPROC		data scaling
REFMAC		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.491→79.44 Å / Cor.coef. F_o:F_c: 0.973 / Cor.coef. F_o:F_c free: 0.947 / SU B: 4.675 / SU ML: 0.072 / Cross valid method: FREE R-VALUE / ESU R: 0.081 / ESU R Free: 0.08
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2148	3512	5.042 %
R_work	0.1478	66149	-
all	0.151	-	-
obs	-	69661	99.404 %

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: 15.729 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.093 Å²	0 Å²	-0 Å²
2-	-	-0.506 Å²	-0 Å²
3-	-	-	1.599 Å²

Refinement step

Cycle: LAST / Resolution: 1.491→79.44 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3282	0	126	398	3806

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.011	3595
X-RAY DIFFRACTION	r_bond_other_d	0.005	0.016	3140
X-RAY DIFFRACTION	r_angle_refined_deg	1.721	1.617	4953
X-RAY DIFFRACTION	r_angle_other_deg	0.585	1.579	7317
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.296	5	488
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	14.269	5	6
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.654	10	505
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	17.595	10	155
X-RAY DIFFRACTION	r_chiral_restr	0.084	0.2	610
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	4414
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	670
X-RAY DIFFRACTION	r_nbd_refined	0.234	0.2	532
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.205	0.2	2912
X-RAY DIFFRACTION	r_nbtor_refined	0.165	0.2	1770
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.089	0.2	1935
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.176	0.2	285
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.146	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined	0.089	0.2	24
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.255	0.2	27
X-RAY DIFFRACTION	r_nbd_other	0.283	0.2	81
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.174	0.2	30
X-RAY DIFFRACTION	r_mcbond_it	2.805	1.447	1898
X-RAY DIFFRACTION	r_mcbond_other	2.805	1.447	1897
X-RAY DIFFRACTION	r_mcangle_it	3.194	2.186	2392
X-RAY DIFFRACTION	r_mcangle_other	3.194	2.186	2393
X-RAY DIFFRACTION	r_scbond_it	5.858	2.032	1697
X-RAY DIFFRACTION	r_scbond_other	5.856	2.032	1698
X-RAY DIFFRACTION	r_scangle_it	7.124	2.911	2557
X-RAY DIFFRACTION	r_scangle_other	7.122	2.912	2558
X-RAY DIFFRACTION	r_lrange_it	6.689	33.114	3796
X-RAY DIFFRACTION	r_lrange_other	6.528	30.286	3703
X-RAY DIFFRACTION	r_rigid_bond_restr	6.053	3	6735

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
1.491-1.529	0.363	246	0.322	4877	0.324	5136	0.887	0.924	99.7469	0.316
1.529-1.571	0.302	264	0.27	4710	0.271	4974	0.917	0.942	100	0.263
1.571-1.617	0.287	233	0.23	4666	0.233	4900	0.928	0.959	99.9796	0.22
1.617-1.666	0.289	245	0.202	4466	0.207	4711	0.933	0.969	100	0.19
1.666-1.721	0.27	212	0.191	4363	0.195	4577	0.946	0.972	99.9563	0.176
1.721-1.781	0.264	242	0.174	4224	0.179	4466	0.954	0.978	100	0.153
1.781-1.849	0.228	224	0.148	4042	0.152	4266	0.969	0.987	100	0.127
1.849-1.924	0.261	184	0.157	3932	0.161	4120	0.959	0.982	99.9029	0.133
1.924-2.01	0.204	184	0.123	3801	0.127	3985	0.975	0.989	100	0.099
2.01-2.108	0.216	173	0.131	3620	0.135	3796	0.969	0.986	99.921	0.105
2.108-2.221	0.214	196	0.112	3414	0.117	3611	0.973	0.992	99.9723	0.094
2.221-2.356	0.216	167	0.131	3234	0.135	3433	0.96	0.986	99.0679	0.108
2.356-2.519	0.198	157	0.099	3081	0.103	3238	0.979	0.989	100	0.085
2.519-2.72	0.187	145	0.11	2725	0.113	2982	0.974	0.992	96.2441	0.098
2.72-2.979	0.179	160	0.117	2637	0.121	2797	0.979	0.991	100	0.111
2.979-3.331	0.169	138	0.115	2390	0.118	2528	0.98	0.992	100	0.111
3.331-3.845	0.16	121	0.117	1923	0.12	2233	0.985	0.991	91.536	0.12
3.845-4.706	0.207	81	0.132	1789	0.135	1931	0.965	0.989	96.841	0.143
4.706-6.644	0.188	100	0.16	1411	0.162	1511	0.985	0.986	100	0.178
6.644-79.44	0.187	40	0.193	844	0.192	884	0.983	0.97	100	0.215

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