PDB-5bn6: Crystal Structure of Frutalin from Artocarpus incisa in complex w...

ID or keywords:

Entry

Database: PDB / ID: 5bn6

Title

Crystal Structure of Frutalin from Artocarpus incisa in complex with galactose

Components

(Jacalin

) x 2

Keywords

SUGAR BINDING PROTEIN / alpha-D-galactose-binding lectin

Function / homology

Function and homology information

carbohydrate binding
Similarity search - Function

Biological species

Artocarpus heterophyllus (jackfruit)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.6499 Å

Authors

Vieira Neto, A.E. / Pereira, H.M. / Moreno, F.B.M.B. / Moreira, A.C.O.M. / Lobo, M.D.P. / Sousa, F.D. / Grangeiro, T.B. / Moreira, R.A.

Citation

Journal: To Be Published
Title: Crystal Structure of Frutalin from Artocarpus incisa in complex with galactose
Authors: Vieira Neto, A.E. / Pereira, H.M. / Moreno, F.B.M.B. / Moreira, A.C.O.M. / Lobo, M.D.P. / Sousa, F.D. / Grangeiro, T.B. / Moreira, R.A.

History

Deposition	May 25, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 8, 2016	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2017	Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2	Jul 29, 2020	Group: Data collection / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3	Sep 27, 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	5bn6.cif.gz	261.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5bn6.ent.gz	208.6 KB	Display	PDB format
PDBx/mmJSON format	5bn6.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bn/5bn6 ftp://data.pdbj.org/pub/pdb/validation_reports/bn/5bn6	HTTPS FTP

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Related structure data

Related structure data	5wogS S: Starting model for refinement
Similar structure data	1ugx-1 1jot-1 1ugy-d 1kuj-d 4ak4-2 1uh0-1 3llz-1 1ugw-d 1uh1-2 4akc-d 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
Related items in Molecule of the Month	#156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (1) #198 - Jun 2016 Beta-galactosidase similarity (1)

Deposited unit

A: Jacalin

E: Jacalin

B: Jacalin

F: Jacalin

C: Jacalin

G: Jacalin

D: Jacalin

H: Jacalin

hetero molecules

68.7 kDa, 8 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)	75.926, 74.606, 119.042
Angle α, β, γ (deg.)	90.000, 96.790, 90.000
Int Tables number	5
Space group name H-M	I121

#1: Protein/peptide

Jacalin /

Mass: 1943.141 Da / Num. of mol.: 4 / Fragment: UNP Residues 61-79 / Source method: isolated from a natural source / Source: (natural)

Artocarpus heterophyllus (jackfruit) / References: UniProt: Q38720

#2: Protein

Jacalin /

Mass: 15061.857 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural)

Artocarpus heterophyllus (jackfruit) / References: UniProt: Q38720

#3: Sugar

ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose /

Galactose

Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C₆H₁₂O₆

#4: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 903 / 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: 2.53 Å³/Da / Density % sol: 51.47 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 10% PEG 20 000, v/v PEG MME 550, 0.1 M bicine/Trizma base pH 8.5

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å

Detector

Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 19, 2014

Radiation

Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Resolution: 1.6499→19.65 Å / Num. all: 77162 / Num. obs: 77162 / % possible obs: 97.3 % / Redundancy: 2.3 % / CC_1/2: 0.998 / R_merge(I) obs: 0.049 / R_pim(I) all: 0.039 / Net I/σ(I): 13.7 / Num. measured all: 174200

Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	CC_1/2	R_pim(I) all	% possible all
1.6499-1.68	1.5	0.446	1.9	4489	2939	0.736	0.395	75.6
9.04-19.65	2.4	0.018	44.7	1040	435	0.999	0.014	85.2

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
d*TREK		data scaling
XDS	0.3.11	data reduction
Aimless		data scaling
PHASER		phasing
PHENIX		refinement
PDB_EXTRACT	3.15	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5WOG

5wog

Resolution: 1.6499→19.65 Å / SU ML: 0.15 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 19.15 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1965	3747	4.86 %	Random selection
R_work	0.1641	73404	-	-
obs	0.1658	77151	97.25 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 63.1 Å² / B_iso mean: 18.5919 Å² / B_iso min: 7.3 Å²

Refinement step

Cycle: final / Resolution: 1.6499→19.65 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4626	0	48	903	5577
B_iso mean	-	-	20.69	31.5	-
Num. residues	-	-	-	-	602

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	4798
X-RAY DIFFRACTION	f_angle_d	1.038	6515
X-RAY DIFFRACTION	f_chiral_restr	0.044	722
X-RAY DIFFRACTION	f_plane_restr	0.005	819
X-RAY DIFFRACTION	f_dihedral_angle_d	10.797	1685

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 (%)
1.6499-1.6708	0.286	107	0.2371	1983	X-RAY DIFFRACTION	71
1.6708-1.6927	0.2619	133	0.2289	2511	X-RAY DIFFRACTION	90
1.6927-1.7159	0.243	123	0.2128	2664	X-RAY DIFFRACTION	96
1.7159-1.7404	0.2143	160	0.1948	2733	X-RAY DIFFRACTION	99
1.7404-1.7664	0.2432	101	0.1909	2808	X-RAY DIFFRACTION	99
1.7664-1.794	0.2247	147	0.1914	2699	X-RAY DIFFRACTION	99
1.794-1.8234	0.2205	134	0.1909	2780	X-RAY DIFFRACTION	99
1.8234-1.8548	0.2382	129	0.1784	2774	X-RAY DIFFRACTION	99
1.8548-1.8885	0.2178	129	0.1772	2763	X-RAY DIFFRACTION	99
1.8885-1.9248	0.2274	139	0.184	2755	X-RAY DIFFRACTION	99
1.9248-1.964	0.201	146	0.1704	2784	X-RAY DIFFRACTION	99
1.964-2.0067	0.2109	126	0.162	2757	X-RAY DIFFRACTION	99
2.0067-2.0533	0.1943	138	0.1554	2765	X-RAY DIFFRACTION	99
2.0533-2.1046	0.1834	150	0.1474	2749	X-RAY DIFFRACTION	99
2.1046-2.1614	0.1761	129	0.1427	2777	X-RAY DIFFRACTION	99
2.1614-2.225	0.1879	127	0.1564	2782	X-RAY DIFFRACTION	99
2.225-2.2967	0.1993	146	0.1623	2767	X-RAY DIFFRACTION	99
2.2967-2.3786	0.1899	109	0.1587	2818	X-RAY DIFFRACTION	99
2.3786-2.4737	0.1888	117	0.1727	2809	X-RAY DIFFRACTION	99
2.4737-2.586	0.2289	126	0.1706	2770	X-RAY DIFFRACTION	99
2.586-2.722	0.2176	158	0.1747	2758	X-RAY DIFFRACTION	99
2.722-2.8921	0.2324	168	0.1773	2729	X-RAY DIFFRACTION	99
2.8921-3.1146	0.1933	179	0.1667	2724	X-RAY DIFFRACTION	99
3.1146-3.4265	0.1722	157	0.1541	2748	X-RAY DIFFRACTION	98
3.4265-3.9189	0.1547	149	0.1524	2735	X-RAY DIFFRACTION	98
3.9189-4.9246	0.1814	145	0.1298	2724	X-RAY DIFFRACTION	97
4.9246-19.6525	0.1851	175	0.1598	2738	X-RAY DIFFRACTION	96

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	0.6313	-1.3969	-0.5054	5.4871	1.9992	1.8961	0.0819	0.1715	-0.3118	0.1325	-0.1305	0.2416	0.1365	-0.1189	0.0073	0.1342	0.0171	-0.0122	0.1403	-0.0215	0.1778	-4.1885	-1.6406	-34.4128
2	0.5942	-0.1584	0.7376	1.388	0.4062	1.52	0.046	0.1397	-0.1271	-0.0272	-0.0874	0.1702	0.0627	-0.1643	0.0238	0.1398	0.0051	-0.0104	0.1218	0.0177	0.1369	-11.0526	8.4479	-40.4546
3	1.5168	-0.6827	0.5113	0.9236	-0.1092	0.9935	0.1085	0.1622	0.0471	-0.2247	-0.1366	-0.0659	-0.0354	0.0402	0.0159	0.1409	0.0308	0.0074	0.1442	0.0222	0.1146	-3.7952	16.2731	-48.4099
4	0.7073	-0.2096	0.0583	0.9512	0.0798	1.2622	-0.0043	-0.0198	0.0461	-0.047	-0.0155	0.0244	-0.116	-0.0798	0.0358	0.1058	0.0219	-0.0061	0.102	0.0055	0.1021	-8.7882	18.4863	-38.2716
5	6.2495	0.2272	2.5175	4.3354	-0.843	2.9519	0.0631	0.6404	0.1366	-0.2385	0.0972	-0.6249	0.0111	0.1372	-0.1668	0.1805	0.0404	0.0195	0.2085	0.0291	0.214	12.4951	5.5962	-23.2064
6	0.757	-0.6609	-0.445	0.7306	0.2416	2.5485	0.091	-0.0436	0.2747	-0.0866	0.0376	-0.3107	-0.1579	0.1673	-0.0395	0.115	-0.0022	0.0014	0.1356	-0.0096	0.1366	-1.2478	20.2667	-22.886
7	0.6332	-0.1424	-0.099	1.5642	-0.0336	0.8576	-0.0296	-0.073	0.0832	0.1012	0.0156	-0.0459	-0.118	-0.0924	-0.0149	0.1333	0.0156	-0.008	0.1444	-0.0234	0.1023	-7.9717	15.139	-10.8735
8	0.7566	-0.0102	0.105	1.8789	-0.0354	0.9866	-0.0485	-0.1282	-0.0018	0.2199	0.0512	-0.0242	-0.0351	-0.018	-0.0027	0.1121	0.0025	0.0103	0.1191	-0.0132	0.0825	-8.1777	9.0319	-9.1084
9	0.7765	-0.0899	0.0967	0.3556	-0.0621	0.9701	-0.0067	-0.0383	0.0669	-0.0226	0.0213	0.03	-0.1012	-0.0649	0.0144	0.1123	0.0136	-0.0029	0.1069	-0.0091	0.1067	-10.2817	17.1542	-19.2357
10	5.3807	-2.7371	-2.5478	3.246	1.2969	1.4311	-0.0736	0.2928	0.0098	0.0438	0.0462	0.3766	0.0741	-0.1688	0.0949	0.1351	0.0151	-0.0027	0.1367	0.0166	0.1587	-1.4584	-5.3154	-23.5731
11	1.2402	-0.8224	-0.5809	1.4394	-0.6721	1.5827	-0.0294	-0.0177	-0.1639	0.0979	-0.0461	0.2709	0.1338	-0.064	0.0877	0.0844	-0.0176	-0.0016	0.1107	0.0048	0.1474	7.1767	-14.777	-17.2049
12	0.3585	-0.2323	-0.1164	1.9954	-0.1409	0.6961	-0.0616	-0.0944	-0.059	0.1682	0.0407	0.0809	0.0863	0.0846	0.005	0.1382	0.021	-0.0035	0.1407	0.02	0.108	15.1608	-11.5037	-8.514
13	0.6235	-0.1698	-0.1992	0.5609	0.2092	1.0321	-0.0387	-0.0252	-0.0538	0.0442	0.0352	0.0061	0.0918	0.0987	-0.0109	0.0933	0.0123	-0.0054	0.0979	0.0074	0.0956	18.1613	-12.8893	-18.3548
14	1.6755	-1.4265	0.4116	7.0028	-2.7729	1.108	0.1842	0.2033	0.2965	0.1424	-0.269	0.0113	-0.1459	0.2371	0.0684	0.1284	0.0221	-0.0012	0.1293	0.0209	0.1322	11.1778	3.8079	-34.5309
15	0.4146	-0.1838	-0.6603	1.4579	-0.398	1.6176	0.0427	0.021	0.1875	-0.0405	-0.1011	-0.1133	-0.048	0.1543	-0.0069	0.1137	0.0079	0.017	0.1107	-0.0041	0.1295	17.9148	-6.138	-40.779
16	1.3953	-0.7067	-0.1103	1.4863	0.0779	1.1101	0.0801	0.1379	-0.0858	-0.2239	-0.1384	0.1114	0.0478	-0.0297	0.0604	0.1302	0.0369	-0.0149	0.12	-0.0187	0.1083	10.3569	-13.2632	-48.087
17	0.9555	-0.3006	-0.092	0.9052	0.0278	0.7727	0.0764	0.2068	0.0445	-0.3267	-0.1064	0.0998	0.038	-0.0261	0.0516	0.1908	0.0336	0.0001	0.1535	-0.0155	0.1366	10.7495	-15.3092	-49.0124
18	0.5556	-0.1247	-0.0333	1.0869	-0.1502	1.1378	0.0113	0.0071	-0.0207	-0.1146	-0.0641	-0.0772	0.0889	0.1073	0.0471	0.0992	0.0242	0.0076	0.1055	-0.0007	0.1084	15.7096	-16.2109	-38.4911

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 12 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 13 through 34 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 35 through 88 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 89 through 157 )	A
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 1 through 9 )	B
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 10 through 25 )	B
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 26 through 51 )	B
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 52 through 88 )	B
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 89 through 157 )	B
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 3 through 12 )	C
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 13 through 34 )	C
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 35 through 75 )	C
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 76 through 157 )	C
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 3 through 12 )	D
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 13 through 34 )	D
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 35 through 64 )	D
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 65 through 88 )	D
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 89 through 157 )	D

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