PDB-6flw: Structure of AcmJRL, a mannose binding jacalin related lectin fro...

ID or keywords:

Entry

Database: PDB / ID: 6flw

Title

Structure of AcmJRL, a mannose binding jacalin related lectin from Ananas comosus.

Components

Jacalin-like lectin

Keywords

SUGAR BINDING PROTEIN /

mannose binding lectin / A. comosus stem

Function / homology

Function and homology information

carbohydrate binding
Similarity search - Function

Biological species

Ananas comosus (pineapple)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Azarkan, M. / Herman, R. / El Mahyaoui, R. / Sauvage, E. / Vanden Broeck, A. / Charlier, P.

Funding support

Belgium, 2items

Citation

Journal: Sci Rep / Year: 2018
Title: Biochemical and structural characterization of a mannose binding jacalin-related lectin with two-sugar binding sites from pineapple (Ananas comosus) stem.
Authors: Azarkan, M. / Feller, G. / Vandenameele, J. / Herman, R. / El Mahyaoui, R. / Sauvage, E. / Vanden Broeck, A. / Matagne, A. / Charlier, P. / Kerff, F.

History

Deposition	Jan 29, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 15, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jan 17, 2024	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

-
Download

PDBx/mmCIF format	6flw.cif.gz	329.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6flw.ent.gz	273.2 KB	Display	PDB format
PDBx/mmJSON format	6flw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fl/6flw ftp://data.pdbj.org/pub/pdb/validation_reports/fl/6flw	HTTPS FTP

-
Related structure data

Related structure data	6flyC 6flzC 1x1vS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6fly-1 6flz-1 6ikm-4 5hhl-4 6uep-d 2coi-d 6ikm-13 3ufx-5 2coj-d 1kt8-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

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Jacalin-like lectin

B: Jacalin-like lectin

C: Jacalin-like lectin

D: Jacalin-like lectin

hetero molecules

61.8 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration, dimer in solution

Unit cell

Length a, b, c (Å)	68.069, 86.013, 88.928
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Jacalin-like lectin Mass: 15360.363 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Ananas comosus (pineapple) / References: UniProt: Q53J09
#2: Chemical	ChemComp-CIT / CITRIC ACID / Citric acid Mass: 192.124 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C₆H₈O₇
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 502 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.12 Å³/Da / Density % sol: 41.94 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 15% PEG3000, 0.1M citrate pH5.5; protein solution 17mg/ml in H2O

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.21458 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 9, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.21458 Å / Relative weight: 1
Reflection	Resolution: 1.8→45.8 Å / Num. obs: 49023 / % possible obs: 100 % / Redundancy: 7.4 % / R_merge(I) obs: 0.103 / Net I/σ(I): 15
Reflection shell	Resolution: 1.8→1.9 Å / Redundancy: 7.3 % / R_merge(I) obs: 0.81 / Mean I/σ(I) obs: 2.7 / % possible all: 100

-
Processing

Software

Name	Version	Classification
PHENIX	(1.10_2152: ???)	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1X1V

1x1v

Resolution: 1.8→44.464 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0.12 / Phase error: 16.13

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.183	2479	5.06 %	Random selection
R_work	0.1461	-	-	-
obs	0.148	49023	99.88 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.8→44.464 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4348	0	26	502	4876

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	4534
X-RAY DIFFRACTION	f_angle_d	0.815	6163
X-RAY DIFFRACTION	f_dihedral_angle_d	11.335	2583
X-RAY DIFFRACTION	f_chiral_restr	0.054	666
X-RAY DIFFRACTION	f_plane_restr	0.004	802

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 (%)
1.8-1.8346	0.2801	139	0.2432	2565	X-RAY DIFFRACTION	100
1.8346-1.8721	0.2737	122	0.215	2536	X-RAY DIFFRACTION	100
1.8721-1.9128	0.2176	135	0.1881	2535	X-RAY DIFFRACTION	100
1.9128-1.9573	0.2312	167	0.1663	2580	X-RAY DIFFRACTION	100
1.9573-2.0062	0.1944	139	0.15	2525	X-RAY DIFFRACTION	100
2.0062-2.0605	0.1806	130	0.1488	2556	X-RAY DIFFRACTION	100
2.0605-2.1211	0.2436	133	0.1468	2559	X-RAY DIFFRACTION	100
2.1211-2.1896	0.2053	133	0.1472	2558	X-RAY DIFFRACTION	100
2.1896-2.2678	0.1781	115	0.1424	2602	X-RAY DIFFRACTION	100
2.2678-2.3586	0.1858	138	0.1415	2557	X-RAY DIFFRACTION	100
2.3586-2.466	0.1947	136	0.1465	2573	X-RAY DIFFRACTION	100
2.466-2.596	0.1774	130	0.1463	2576	X-RAY DIFFRACTION	100
2.596-2.7586	0.1836	129	0.152	2606	X-RAY DIFFRACTION	100
2.7586-2.9715	0.208	146	0.1469	2590	X-RAY DIFFRACTION	100
2.9715-3.2705	0.1524	150	0.1417	2582	X-RAY DIFFRACTION	100
3.2705-3.7435	0.153	154	0.1232	2620	X-RAY DIFFRACTION	100
3.7435-4.7156	0.1406	141	0.1125	2647	X-RAY DIFFRACTION	100
4.7156-44.4775	0.1779	142	0.1587	2777	X-RAY DIFFRACTION	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	1.8637	-0.4952	0.5052	3.5107	-1.0671	2.7689	-0.0073	0.2075	0.0256	-0.1066	0.0518	-0.0066	0.0329	0.0499	-0.1038	0.0985	-0.0249	0.0082	0.0791	0.0053	0.0924	2.3541	10.3813	1.9733
2	2.0612	-0.5539	1.7057	0.1734	-0.4897	1.4454	-0.0996	0.3206	0.2553	0.0229	-0.0664	-0.0326	-0.1609	0.2819	0.1412	0.1437	-0.0024	-0.0017	0.1643	0.0374	0.161	10.8793	17.8201	4.6099
3	7.9896	-3.9585	2.1915	2.0501	-1.0909	0.6389	-0.1092	-0.2543	0.5552	-0.0373	-0.067	-0.1203	-0.091	-0.0811	0.1128	0.1683	0.0054	0.0001	0.1211	-0.0402	0.1711	1.6373	23.1309	14.2056
4	1.5444	-0.6373	0.7076	1.1817	-0.3128	0.5059	-0.1086	0.1996	0.4706	0.0029	-0.0162	-0.0291	-0.052	0.0132	0.0774	0.1667	0.0076	0.0072	0.1371	0.0076	0.175	4.8769	23.781	9.2438
5	3.1431	-2.8518	3.0043	4.1063	-2.3348	3.3098	-0.1354	-0.3432	0.218	0.2914	0.1431	0.0916	-0.169	-0.1912	0.0206	0.1405	-0.0005	0.0423	0.1669	-0.0453	0.1618	4.0313	20.3687	21.2817
6	3.7512	-0.7696	2.1632	1.5792	-0.6227	3.289	0.026	0.0721	-0.0574	0.0406	0.0832	0.3647	-0.0953	-0.1753	-0.1171	0.0964	-0.0025	0.0058	0.0837	0.0064	0.1683	-7.2262	13.4794	10.0608
7	1.1234	-0.038	0.1075	0.8537	-0.3617	1.1005	0.0038	-0.0536	0.1012	0.0738	0.0242	0.074	-0.0606	-0.0396	-0.0237	0.1194	-0.0006	-0.0015	0.0835	-0.0094	0.1245	0.7376	12.5589	12.2968
8	1.2241	0.3893	0.8724	2.7013	-0.2896	0.7508	-0.2722	-0.5107	-0.2331	0.3651	0.131	-0.0334	0.0979	0.0101	0.0772	0.2066	0.041	0.0265	0.1521	0.0376	0.1264	3.1203	-3.3426	16.9878
9	2.1124	0.8072	-1.1146	0.8642	-0.2568	0.75	-0.1438	-0.1674	-0.3814	0.1152	0.0414	-0.1044	0.105	0.1532	0.0506	0.1657	0.018	0.005	0.1346	0.0304	0.2061	7.1177	-12.5854	9.4548
10	1.8686	0.7761	-0.5454	0.9231	-0.1789	0.6536	-0.2984	-0.2969	-0.6455	0.0421	0.1325	0.1347	0.1094	0.0499	0.1295	0.1676	-0.0023	0.0477	0.1029	0.0333	0.2451	4.8856	-16.5858	9.288
11	2.9454	0.5577	-1.967	1.4012	-0.9945	2.4417	-0.0723	0.192	-0.2481	-0.2799	-0.0248	0.0544	0.0715	-0.0385	0.0846	0.1404	-0.0238	-0.016	0.1404	-0.0208	0.1237	1.043	-9.5286	-0.0832
12	1.9092	-0.2211	0.2792	1.9014	-0.2396	0.7763	-0.0792	-0.0748	-0.1248	0.0515	0.0977	0.1806	0.0608	-0.0836	-0.0082	0.1399	-0.0101	0.0118	0.1027	0.0044	0.1211	-2.1001	-6.2583	8.1949
13	1.3343	-0.332	0.5517	0.5908	0.1513	1.1294	0.0125	-0.143	-0.0477	0.0186	0.0226	0.0654	0.0453	-0.07	-0.0285	0.1277	0.0007	0.0005	0.1408	0.009	0.0871	-36.6397	6.3371	22.1459
14	2.6658	-0.5752	0.4249	0.5673	-0.3798	0.9287	-0.0955	-0.3414	0.2057	0.1057	0.0483	-0.04	-0.1011	0.092	0.016	0.1501	-0.0028	-0.0224	0.1906	-0.0297	0.1042	-36.0234	12.3376	27.6941
15	2.3282	-0.8684	1.4987	1.2895	-1.1092	2.0169	-0.032	-0.0166	0.3322	-0.0565	-0.0745	-0.0412	-0.2476	0.0941	0.0858	0.1111	-0.0175	-0.003	0.1191	0.0103	0.126	-32.019	17.8186	17.506
16	1.6018	0.0124	0.3245	1.1326	-0.0132	1.5474	-0.0113	-0.0698	0.0582	0.0821	0.0092	-0.0733	-0.0435	0.1424	0.0106	0.1067	0.0014	-0.005	0.1207	0.0004	0.0803	-29.1825	9.0922	17.8658
17	1.8462	0.5666	-1.1643	1.3945	-0.4885	2.0741	0.0223	0.0686	0.3155	-0.14	0.0206	0.0465	-0.0616	0.0566	-0.0215	0.1413	0.0083	0.0101	0.1233	0.0014	0.0953	-32.9773	7.8146	-0.6749
18	2.6789	0.7888	-1.4309	0.3583	-0.2208	1.0514	-0.0908	0.3501	-0.1427	-0.0792	0.1223	0.1383	0.0224	-0.143	-0.0077	0.1357	-0.0012	0.0008	0.1577	-0.0185	0.1141	-38.078	-3.1136	-5.732
19	6.279	0.7939	-1.0568	0.7575	0.0963	0.581	-0.1465	0.199	-0.0365	-0.1227	0.1044	-0.0642	0.1196	0.0266	-0.0077	0.1425	0.0158	-0.0017	0.1787	-0.0076	0.1148	-33.3379	-5.2443	-6.7779
20	4.1762	0.1375	-2.0999	0.1862	-0.1363	1.5604	-0.3471	0.8507	-0.3035	-0.0406	0.1873	-0.0706	0.0747	-0.2597	0.1808	0.1668	-0.0075	0.0169	0.2355	-0.0724	0.1559	-38.7635	-5.4137	-10.703
21	2.495	0.3344	-0.6304	0.4977	-0.054	1.1452	-0.0016	-0.0064	-0.5324	-0.1011	-0.141	-0.1988	0.2722	0.0868	0.1087	0.152	0.0403	0.023	0.0919	0.0024	0.2084	-32.8446	-11.038	2.0121
22	1.5143	0.0415	-0.2999	0.7631	-0.0762	1.6698	0.0109	-0.0137	-0.0624	-0.0408	-0.0077	-0.063	0.0728	0.1731	0.0051	0.1211	0.0195	0.0054	0.1123	-0.0122	0.1097	-27.402	-2.8437	1.9037
23	1.6526	0.1754	-1.1621	0.7366	-0.0321	1.9517	-0.0761	0.1036	-0.0607	-0.0979	0.0205	0.0323	0.1765	-0.0137	0.044	0.1239	0.0081	0.0027	0.1386	-0.0048	0.0994	-35.6987	0.7811	0.2948

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 15 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 16 through 26 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 27 through 34 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 35 through 62 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 63 through 74 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 75 through 99 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 100 through 145 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 2 through 15 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 16 through 34 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 35 through 62 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 63 through 82 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 83 through 145 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 2 through 34 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 35 through 62 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 63 through 82 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 83 through 145 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 2 through 15 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 16 through 34 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 35 through 47 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 48 through 62 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 63 through 82 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 83 through 131 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 132 through 145 )

-
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

-
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

-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

-
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