PDB-3zyh: CRYSTAL STRUCTURE OF PA-IL LECTIN COMPLEXED WITH GALBG0 AT 1.5 A ...

ID or keywords:

Entry

Database: PDB / ID: 3zyh

Title

CRYSTAL STRUCTURE OF PA-IL LECTIN COMPLEXED WITH GALBG0 AT 1.5 A RESOLUTION

Components

PA-I galactophilic lectin

Keywords

SUGAR BINDING PROTEIN/INHIBITOR / SUGAR BINDING PROTEIN-INHIBITOR COMPLEX / ADHESIN / GLYCOSPHINGOLIPID-ANTIGEN / GALACTOSE-SPECIFIC /

GALACTOSIDES

Function / homology

Function and homology information

heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules /

carbohydrate binding /

periplasmic space /

cell surface /

cytoplasm
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)
SYNTHETIC CONSTRUCT (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.501 Å

Authors

Kadam, R.U. / Bergmann, M. / Hurley, M. / Garg, D. / Cacciarini, M. / Swiderska, M.A. / Nativi, C. / Sattler, M. / Smyth, A.R. / Williams, P. ...

Citation

Journal: Angew.Chem.Int.Ed.Engl. / Year: 2011
Title: A Glycopeptide Dendrimer Inhibitor of the Galactose Specific Lectin Leca and of Pseudomonas Aeruginosa Biofilms
Authors: Kadam, R.U. / Bergmann, M. / Hurley, M. / Garg, D. / Cacciarini, M. / Swiderska, M.A. / Nativi, C. / Sattler, M. / Smyth, A.R. / Williams, P. / Camara, M. / Stocker, A. / Darbre, T. / Reymond, J.-L.

History

Deposition	Aug 23, 2011	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 21, 2011	Provider: repository / Type: Initial release
Revision 1.1	Sep 28, 2011	Group: Database references
Revision 1.2	Oct 5, 2011	Group: Atomic model / Other
Revision 1.3	Oct 26, 2011	Group: Atomic model
Revision 1.4	Nov 16, 2011	Group: Database references
Revision 1.5	Nov 30, 2012	Group: Other
Revision 1.6	Sep 16, 2015	Group: Source and taxonomy
Revision 1.7	Aug 2, 2017	Group: Structure summary / Category: pdbx_molecule_features
Revision 1.8	Oct 2, 2019	Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other Category: exptl_crystal_grow / pdbx_database_status ...exptl_crystal_grow / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_prop Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.value
Revision 1.9	Jul 29, 2020	Group: Data collection / Derived calculations Category: chem_comp / struct_conn ...chem_comp / struct_conn / struct_site / struct_site_gen Item: _chem_comp.type / _struct_conn.pdbx_dist_value ..._chem_comp.type / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.10	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3zyh.cif.gz	122 KB	Display	PDBx/mmCIF format
PDB format	pdb3zyh.ent.gz	93.5 KB	Display	PDB format
PDBx/mmJSON format	3zyh.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/zy/3zyh ftp://data.pdbj.org/pub/pdb/validation_reports/zy/3zyh	HTTPS FTP

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Related structure data

Related structure data	3zybC 3zyfC 1l7lS 1oko 1uoj 2vxj 2wyf S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4a6s-1 2wyf-1 3zyf-2 3zyf-1 4cpb-2 4a6s-2 6yoh-2 4lk7-3 2wyf-4 2wyf-3 Search similar-shape structures by Omokage search (details) 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: PA-I galactophilic lectin

B: PA-I galactophilic lectin

hetero molecules

26.4 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)	40.559, 72.865, 133.723
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P22₁2₁

#1: Protein	PA-I galactophilic lectin / PA-IL / Galactose-binding lectin Mass: 12901.333 Da / Num. of mol.: 2 / Fragment: MAINLY BETA SANDWICH Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: lecA, pa1L, PA2570 / Plasmid: PET25PAIL / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q05097
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Sugar	ChemComp-G0S / 3-(beta-D-galactopyranosylthio)propanoic acid / 3-(beta-D-galactosylthio)propanoic acid / 3-(D-galactosylthio)propanoic acid / 3-(galactosylthio)propanoic acid Type: D-saccharide / Mass: 268.284 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₉H₁₆O₇S / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 646 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.94 Å³/Da / Density % sol: 58.1 % / Description: NONE
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 1.5 M AMMONIUM SULFATE AND 0.1 M SODIUM ACETATE PH 4.6.

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 2, 2010
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.5→66.86 Å / Num. obs: 61876 / % possible obs: 96.1 % / Observed criterion σ(I): 3 / Redundancy: 3.5 % / B_iso Wilson estimate: 16.8 Å² / R_merge(I) obs: 0.03 / Net I/σ(I): 34.5
Reflection shell	Resolution: 1.5→1.59 Å / Redundancy: 2.9 % / R_merge(I) obs: 0.07 / Mean I/σ(I) obs: 14.8 / % possible all: 84.2

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1L7L

1l7l

Resolution: 1.501→49.264 Å / SU ML: 0.15 / σ(F): 2.07 / Phase error: 16.18 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2015	3087	5 %
R_work	0.1855	-	-
obs	0.1863	61836	96.12 %

Solvent computation

Shrinkage radii: 0.53 Å / VDW probe radii: 0.7 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 65.823 Å² / k_sol: 0.464 e/Å³

Displacement parameters

B_iso mean: 14.9 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.1539 Å²	0 Å²	0 Å²
2-	-	-0.539 Å²	0 Å²
3-	-	-	-2.615 Å²

Refinement step

Cycle: LAST / Resolution: 1.501→49.264 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1830	0	2	646	2478

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	1890
X-RAY DIFFRACTION	f_angle_d	1.108	2588
X-RAY DIFFRACTION	f_dihedral_angle_d	16.528	692
X-RAY DIFFRACTION	f_chiral_restr	0.135	284
X-RAY DIFFRACTION	f_plane_restr	0.005	342

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 (%)
1.5008-1.5243	0.2083	105	0.175	1992	X-RAY DIFFRACTION	73
1.5243-1.5493	0.2029	119	0.1768	2261	X-RAY DIFFRACTION	82
1.5493-1.576	0.2092	129	0.1788	2460	X-RAY DIFFRACTION	90
1.576-1.6046	0.229	141	0.1764	2685	X-RAY DIFFRACTION	98
1.6046-1.6355	0.2002	142	0.1704	2714	X-RAY DIFFRACTION	99
1.6355-1.6689	0.1965	143	0.1699	2734	X-RAY DIFFRACTION	100
1.6689-1.7052	0.1959	144	0.165	2725	X-RAY DIFFRACTION	99
1.7052-1.7449	0.1886	143	0.1695	2728	X-RAY DIFFRACTION	99
1.7449-1.7885	0.1988	144	0.1722	2723	X-RAY DIFFRACTION	99
1.7885-1.8369	0.2033	145	0.1707	2761	X-RAY DIFFRACTION	100
1.8369-1.8909	0.1918	144	0.1717	2727	X-RAY DIFFRACTION	100
1.8909-1.9519	0.1749	144	0.1683	2744	X-RAY DIFFRACTION	99
1.9519-2.0217	0.176	145	0.1713	2767	X-RAY DIFFRACTION	99
2.0217-2.1027	0.1985	143	0.1742	2726	X-RAY DIFFRACTION	99
2.1027-2.1983	0.2083	145	0.1863	2742	X-RAY DIFFRACTION	99
2.1983-2.3142	0.2105	145	0.1817	2758	X-RAY DIFFRACTION	99
2.3142-2.4592	0.1898	144	0.1815	2746	X-RAY DIFFRACTION	99
2.4592-2.6491	0.2002	144	0.1894	2746	X-RAY DIFFRACTION	98
2.6491-2.9157	0.228	147	0.1924	2796	X-RAY DIFFRACTION	99
2.9157-3.3375	0.174	145	0.1933	2760	X-RAY DIFFRACTION	98
3.3375-4.2045	0.2213	144	0.1875	2732	X-RAY DIFFRACTION	95
4.2045-49.2907	0.2118	142	0.2344	2722	X-RAY DIFFRACTION	90

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	0.0271	-0	-0.0104	0.0128	0.0017	0.0049	-0.108	-0.0698	-0.0002	-0.0477	0.0539	0.0723	0.0609	0.0229	-0.0012	0.1003	0.0093	0.0284	0.1578	0.0071	0.0689	0.0265	-27.4693	-12.8688
2	0.0311	0.0262	0.0187	0.026	0.0106	0.0819	0.0393	-0.0002	0.0389	0.0522	0.0117	0.0062	-0.0262	-0.0389	0	0.0736	0.0086	0.0064	0.0694	0.0038	0.0585	6.4385	-23.5744	-15.8494
3	-0.0024	0.0001	0.0398	0.0169	0.0169	0.0156	-0.0245	0.0077	0.0114	-0.2034	0.0067	-0.0289	0.0321	-0.0919	-0	0.0823	0.0098	-0.0179	0.0738	0.0126	0.0655	6.9074	-28.6133	-32.2812
4	0.0065	-0.0022	0.0021	0.0255	-0.0037	0.0046	-0.1211	0.0823	-0.1824	-0.1864	-0.0015	-0.0728	0.1363	0.18	-0	0.0773	0.0047	0.0255	0.0844	0.0257	0.0692	15.631	-26.3683	-35.0371
5	0.01	0.0238	-0.0238	0.0291	0.0158	0.0185	-0.0261	0.0916	0.0414	-0.0953	0.0627	0.0592	0.0351	-0.0622	0	0.0552	-0.0002	0.0043	0.0557	0.0196	0.0676	14.8819	-20.1562	-26.99
6	0.1128	0.0121	0.0749	0.004	0.0136	0.0763	0.0479	-0.0017	0.1971	0.2022	-0.0541	-0.0375	-0.1696	-0.0711	-0.0172	0.1131	-0.0037	0.013	0.0655	-0.0036	0.0889	13.7223	-17.2764	-14.7287
7	0.0433	0.0118	-0.0306	0.016	0.0134	0.0414	-0.0021	-0.0104	0.2058	0.0578	-0.103	0.0686	0.0085	0.1675	-0.0006	0.0631	0.0005	-0.0088	0.0693	-0.0013	0.0815	16.8257	-26.9718	-11.1749
8	0.0109	0.0058	0.0066	0.0097	0.0078	0.0068	-0.0242	-0.0732	0.1009	-0.0045	-0.0537	-0.3366	-0.313	0.0621	-0	0.1586	-0.0331	0.001	0.107	-0.0098	0.1163	11.1222	-17.3911	-8.7899
9	0.0233	0.0191	0.0153	0.0601	0.0508	0.0415	0.0314	-0.0158	0.0857	0.0478	0.0077	0.048	-0.0236	-0.0155	0	0.05	0.0048	-0.0085	0.0633	0.0183	0.0803	5.2701	-19.4221	-27.429
10	-0.0061	-0.0198	-0.0013	0.0159	0.0091	0.0116	-0.0231	-0.0673	0.01	0.088	0.0391	0.1248	0.0012	0.0406	0.0002	0.104	0.0198	0.0087	0.092	0.0192	0.0531	7.7862	-30.5017	-7.8592
11	0.0174	-0.0085	0.0026	0.0089	0.0041	0.0109	0.0096	-0.2342	0.2018	0.0508	0.216	-0.1234	-0.0834	0.0305	0	0.1169	-0.0003	-0.0201	0.1352	-0.0196	0.0823	20.896	-42.8205	-14.592
12	0.065	-0.0592	0.0342	0.0716	0.0863	0.0932	0.041	0.0013	-0.0283	0.0357	0.0015	0.0005	0.0703	0.0599	0	0.0691	0.0109	-0.0181	0.0518	-0.0133	0.0497	14.3503	-46.0905	-18.0629
13	0.0078	0.0066	0.002	0.0376	-0.0008	0.0088	-0.0632	0.1053	0.0264	-0.1107	0.0584	-0.0211	-0.0579	-0.024	-0	0.0585	-0.0093	0.0164	0.0698	-0.0164	0.0544	13.4567	-38.1584	-33.2892
14	0.0019	0.0022	-0.0093	0.0177	0.0043	0.008	-0.1027	-0.0228	-0.0766	-0.1865	0.0187	0.0407	0.0326	-0.0507	0.0001	0.0778	0.0166	-0.0228	0.0751	-0.0035	0.0558	4.5726	-39.8576	-36.074
15	0.0441	0.0129	-0.0303	0.0491	0.0173	0.0153	0.024	0.1136	0.0378	-0.0143	-0.0432	0.0805	0.068	0.0268	-0	0.0448	-0.0039	-0.0131	0.0538	-0.0164	0.0699	5.6002	-47.4027	-29.3421
16	0.0566	0.0322	0.0363	0.0279	0.0141	0.0412	0.0512	-0.0553	-0.041	0.0108	-0.0411	0.0152	0.216	-0.0425	0.0212	0.1184	-0.0117	-0.0113	0.0488	0.0102	0.0621	7.0838	-52.4526	-17.8538
17	0.0379	-0.0632	0.0295	0.0417	-0.0108	0.0583	-0.0719	0.007	-0.1777	0.0539	-0.0157	0.1492	0.0035	-0.251	-0.0008	0.0721	-0.0078	0.0174	0.0864	0.0059	0.0899	4.1628	-43.5286	-12.5605
18	0.0039	0.0006	-0.0103	0.0129	0.0091	0.0081	0.1358	0.1674	-0.1789	0.1519	-0.0825	0.263	0.1831	-0.2546	0.0001	0.1052	-0.0133	-0.0002	0.072	0.0037	0.118	9.8188	-53.3873	-12.0898
19	0.0073	-0.0183	-0.0196	0.0505	0.0469	0.0105	-0.0012	0.0015	-0.0427	0.0084	0.0222	-0.0186	0.0633	0.0334	0	0.0393	0.0037	-0.0048	0.0545	-0.0163	0.0504	15.1679	-48.0722	-30.2298
20	-0.0248	-0.0124	-0.029	-0.0056	0.0057	0.0075	0.0036	0.0565	0.0053	0.1069	0.0278	-0.0371	0.0218	0.0346	0.0001	0.0851	0.0082	-0.0142	0.0633	0.0004	0.0614	13.296	-40.721	-8.9368

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 1:5)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 6:36)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 37:46)
4	X-RAY DIFFRACTION	4	(CHAIN A AND RESID 47:51)
5	X-RAY DIFFRACTION	5	(CHAIN A AND RESID 52:66)
6	X-RAY DIFFRACTION	6	(CHAIN A AND RESID 67:76)
7	X-RAY DIFFRACTION	7	(CHAIN A AND RESID 77:89)
8	X-RAY DIFFRACTION	8	(CHAIN A AND RESID 90:95)
9	X-RAY DIFFRACTION	9	(CHAIN A AND RESID 96:112)
10	X-RAY DIFFRACTION	10	(CHAIN A AND RESID 113:121)
11	X-RAY DIFFRACTION	11	(CHAIN B AND RESID 1:5)
12	X-RAY DIFFRACTION	12	(CHAIN B AND RESID 6:36)
13	X-RAY DIFFRACTION	13	(CHAIN B AND RESID 37:46)
14	X-RAY DIFFRACTION	14	(CHAIN B AND RESID 47:51)
15	X-RAY DIFFRACTION	15	(CHAIN B AND RESID 52:66)
16	X-RAY DIFFRACTION	16	(CHAIN B AND RESID 67:76)
17	X-RAY DIFFRACTION	17	(CHAIN B AND RESID 77:89)
18	X-RAY DIFFRACTION	18	(CHAIN B AND RESID 90:95)
19	X-RAY DIFFRACTION	19	(CHAIN B AND RESID 96:112)
20	X-RAY DIFFRACTION	20	(CHAIN B AND RESID 113:121)

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