PDB-4wog: Crystal Structure of Frutalin from Artocarpus incisa

ID or keywords:

Entry

Database: PDB / ID: 4wog

Title

Crystal Structure of Frutalin from Artocarpus incisa

Components

Frutalin

Keywords

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

Function / homology

Function and homology information

carbohydrate binding
Similarity search - Function

Biological species

Artocarpus incisa (plant)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.813 Å

Authors

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

History

Deposition	Oct 15, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 28, 2015	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 2017	Group: Data collection / Derived calculations / Refinement description Category: diffrn_detector / pdbx_struct_oper_list / software Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2	Sep 27, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4wog.cif.gz	254.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4wog.ent.gz	205.3 KB	Display	PDB format
PDBx/mmJSON format	4wog.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/wo/4wog ftp://data.pdbj.org/pub/pdb/validation_reports/wo/4wog	HTTPS FTP

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Related structure data

Related structure data	3p8sS S: Starting model for refinement
Similar structure data	4ak4-3 4r6p-d 5jm1-d 1ws4-d 4akb-d 4r6q-d 5j51-d 4r6n-d 4r6o-d 3lm1-2 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: Frutalin

B: Frutalin

C: Frutalin

D: Frutalin

67.9 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)	76.170, 74.360, 118.986
Angle α, β, γ (deg.)	90.000, 96.570, 90.000
Int Tables number	5
Space group name H-M	I121

#1: Protein	Frutalin Mass: 16986.986 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Artocarpus incisa (plant) / References: UniProt: A0A0R4I968*PLUS
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 744 / 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, sitting drop / pH: 8.5 Details: 12.5% PEG 1000, 12.5% PEG 3350, 12.5% MPD, 30mM Ethylene Glycols, 100mM Bicine/Tris pH 8.5. (E12 Morpheus)

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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: Oct 6, 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: 1.81→27.02 Å / Num. obs: 59769 / % possible obs: 99.8 % / Redundancy: 4 % / B_iso Wilson estimate: 14.91 Å² / CC_1/2: 0.996 / R_merge(I) obs: 0.087 / R_pim(I) all: 0.049 / Net I/σ(I): 10.3 / Num. measured all: 240259 / Scaling rejects: 146

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
1.81-1.85	3.7	0.456	2.6	12493	3386	0.784	0.271	97
9.06-27.02	3.9	0.042	20.4	1936	494	0.998	0.023	96.1

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
d*TREK		data scaling
Aimless	0.2.17	data scaling
PHASER		phasing
PHENIX		refinement
PDB_EXTRACT	3.15	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3P8S

3p8s

Resolution: 1.813→26.742 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.22 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2026	2879	4.82 %	Random selection
R_work	0.161	56883	-	-
obs	0.163	59762	99.81 %	-

Solvent computation

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

Displacement parameters

B_iso max: 88.14 Å² / B_iso mean: 19.3262 Å² / B_iso min: 6.61 Å²

Refinement step

Cycle: final / Resolution: 1.813→26.742 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4626	0	0	744	5370
B_iso mean	-	-	-	32.15	-
Num. residues	-	-	-	-	602

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4750
X-RAY DIFFRACTION	f_angle_d	1.017	6447
X-RAY DIFFRACTION	f_chiral_restr	0.041	702
X-RAY DIFFRACTION	f_plane_restr	0.005	819
X-RAY DIFFRACTION	f_dihedral_angle_d	10.939	1641

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.813-1.8427	0.2909	122	0.235	2578	2700	96
1.8427-1.8745	0.259	165	0.2107	2664	2829	100
1.8745-1.9086	0.2686	145	0.204	2722	2867	100
1.9086-1.9453	0.2576	134	0.1788	2701	2835	100
1.9453-1.9849	0.2251	119	0.1607	2681	2800	100
1.9849-2.0281	0.2054	155	0.1602	2727	2882	100
2.0281-2.0753	0.202	141	0.154	2677	2818	100
2.0753-2.1271	0.2138	126	0.1557	2757	2883	100
2.1271-2.1846	0.2092	144	0.1526	2686	2830	100
2.1846-2.2489	0.2157	127	0.1583	2718	2845	100
2.2489-2.3214	0.2248	145	0.1633	2694	2839	100
2.3214-2.4043	0.2128	116	0.1675	2694	2810	100
2.4043-2.5005	0.2126	124	0.1709	2736	2860	100
2.5005-2.6142	0.2249	119	0.1709	2727	2846	100
2.6142-2.7519	0.2098	118	0.1743	2731	2849	100
2.7519-2.9242	0.2428	135	0.1784	2713	2848	100
2.9242-3.1496	0.1921	138	0.1605	2713	2851	100
3.1496-3.466	0.1693	139	0.1548	2750	2889	100
3.466-3.9661	0.1719	163	0.1507	2705	2868	100
3.9661-4.9916	0.1611	160	0.1248	2713	2873	100
4.9916-26.7452	0.1965	144	0.1566	2796	2940	100

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	1.5121	-1.9141	-0.4256	8.1383	2.934	1.7654	0.057	0.1878	-0.3678	0.1681	-0.0381	0.1273	0.0743	0.1249	-0.0878	0.1162	0.0501	-0.0099	0.148	-0.0253	0.1619	-4.299	-1.7204	-34.3873
2	1.0367	-0.717	0.87	2.5999	0.8342	2.4101	0.0602	0.0975	-0.2405	-0.0562	-0.1807	0.2527	0.0008	-0.2259	0.0742	0.1042	0.0063	-0.006	0.1163	0.025	0.1174	-11.1766	8.3117	-40.4252
3	2.4468	-1.0738	0.6632	1.7181	-0.2559	1.5588	0.155	0.1715	0.0146	-0.2627	-0.1629	-0.0395	-0.0292	-0.0527	0.0072	0.1405	0.0427	0.0032	0.1249	0.0101	0.0792	-6.4759	15.0625	-49.3366
4	1.0845	-0.3688	0.1821	1.3958	-0.1245	1.36	0.0116	0.0216	0.0531	-0.1162	-0.0498	-0.0236	-0.1104	-0.0873	0.0293	0.0937	0.0266	-0.0043	0.0858	0.0085	0.0833	-6.9016	18.5634	-39.46
5	8.6668	-1.5442	3.6257	4.2671	2.9291	4.7194	0.5205	0.9157	0.4054	-0.4041	0.1026	-0.9991	0.09	0.3205	-0.4859	0.1968	0.0259	0.0261	0.1614	0.0321	0.2925	12.5044	5.6869	-23.1237
6	1.8069	-0.9057	-1.1981	1.8767	0.6397	3.5343	0.1559	-0.1366	0.4902	0.0268	-0.0503	-0.4374	-0.1616	0.2073	-0.1039	0.1164	-0.0044	-0.0205	0.1334	-0.0223	0.1405	-1.4474	20.2434	-22.8737
7	1.3151	-0.5662	-0.339	3.7693	0.2634	1.4903	-0.0092	-0.124	0.031	0.0881	0.0222	0.0867	-0.1503	-0.0576	-0.0118	0.1141	-0.0013	-0.0115	0.1202	-0.018	0.0594	-8.1681	15.0794	-10.9055
8	1.0331	-0.1487	0.0093	2.5135	0.3198	0.9105	-0.042	-0.1608	0.014	0.1753	0.0573	-0.0396	-0.1048	-0.0822	-0.0151	0.1124	0.0006	0.0104	0.1215	-0.0117	0.0583	-8.3372	8.9957	-9.124
9	1.2534	-0.136	0.0102	1.0379	0.2502	1.5302	-0.0042	-0.0782	0.0702	-0.005	0.0453	0.0026	-0.1294	-0.0555	-0.0414	0.0927	0.0103	-0.008	0.0901	-0.0059	0.0769	-10.4892	17.0673	-19.2694
10	7.3654	-4.3304	-3.5579	4.0194	1.8444	1.7909	-0.1061	0.2513	-0.1068	-0.026	0.0441	0.4979	0.0746	-0.1972	0.0414	0.1104	0.0179	-0.0141	0.1288	0.0166	0.1932	-1.5549	-5.3659	-23.4967
11	1.9135	-1.4405	-0.9624	2.3747	-0.4842	2.8374	-0.1255	0.0275	-0.2672	0.2189	-0.06	0.3219	0.3039	-0.0836	0.1536	0.0805	-0.0309	-0.0069	0.0977	0.0158	0.1352	7.176	-14.7646	-17.199
12	0.9724	-0.4107	-0.1736	2.959	0.0319	0.8976	-0.0643	-0.1031	0.0321	0.2563	0.0342	-0.0269	0.0589	0.1155	0.016	0.1115	0.0212	-0.0227	0.1251	0.0206	0.0643	15.9211	-8.9277	-9.8972
13	0.6959	0.149	0.1133	5.6156	-1.828	1.7433	-0.1595	-0.2713	-0.1907	0.4731	0.1092	0.4062	0.1661	0.1968	-0.0336	0.2389	0.0456	0.024	0.1984	0.0379	0.1203	12.9861	-18.5527	-4.576
14	0.6979	-0.195	-0.1949	1.3167	0.0869	1.2183	-0.0273	-0.0845	-0.0585	0.0521	0.0281	-0.0632	0.1196	0.1637	0.0083	0.0869	0.0147	-0.0107	0.1088	0.0039	0.0991	19.7988	-12.2	-18.5772
15	2.2038	-2.2489	1.2424	4.0251	-1.6458	3.0935	-0.0289	-0.0679	-0.1533	0.104	-0.0088	0.1582	0.1123	0.0461	0.0123	0.0867	0.0122	0.0256	0.0892	0.0132	0.1109	10.8499	-15.6754	-17.4005
16	3.0772	-2.156	1.1482	3.4731	-3.5666	4.3043	0.097	0.1475	0.343	0.4648	-0.1116	-0.0961	-0.4585	-0.0454	-0.139	0.1543	0.0375	0.0038	0.1361	0.0136	0.1454	11.0263	3.9082	-34.4867
17	0.7399	-0.6862	-0.4017	2.886	-0.4481	2.78	0.0844	0.12	0.187	-0.1172	-0.1507	-0.2001	-0.0819	0.2564	0.0781	0.1199	-0.0017	0.0277	0.1299	0.0083	0.1269	17.8401	-6.1411	-40.7987
18	1.8517	-0.8331	-0.0704	2.2645	-0.0644	1.024	0.252	0.2733	0.0712	-0.4711	-0.2813	-0.0967	0.0245	0.0807	0.0225	0.1912	0.0645	0.0039	0.1544	-0.0046	0.0922	12.933	-12.9888	-49.4706
19	0.559	-0.5189	-0.1794	1.6937	0.1394	1.4401	0.0423	0.0514	-0.0511	-0.1773	-0.0906	0.0219	0.1444	0.0659	0.0398	0.1019	0.0285	0.0025	0.1016	-0.0075	0.1032	12.5345	-17.8536	-39.3969
20	2.4442	-2.0996	-1.3568	3.385	1.7262	3.5435	0.1062	0.0793	0.1082	-0.2829	-0.0642	-0.1699	-0.0729	0.0997	-0.0221	0.0997	0.0171	0.0228	0.0916	0.0279	0.1049	17.9025	-9.8334	-40.5001

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 75 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 76 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 64 )	C
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 65 through 75 )	C
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 76 through 144 )	C
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 145 through 157 )	C
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 3 through 12 )	D
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 13 through 34 )	D
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 35 through 75 )	D
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 76 through 144 )	D
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 145 through 157 )	D

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