PDB-8b97: N-terminal beta-trefoil lectin domain of the Laccaria bicolor lec...

ID or keywords:

Entry

Database: PDB / ID: 8b97

Title

N-terminal beta-trefoil lectin domain of the Laccaria bicolor lectin in complex with N-acetyl-lactosamine

Components

Beta-trefoil domain of the LBL lectin

Keywords

SUGAR BINDING PROTEIN / atomic resolution / beta-trefoil / fruiting-body lectin / sugar-specificity

Function / homology

Ricin B-like lectins / N-acetyl-alpha-lactosamine / Predicted protein

Function and homology information

Biological species

Laccaria bicolor S238N-H53 (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 0.97 Å

Authors

Acebron, I. / Campanero-Rhodes, M.A. / Solis, D. / Menendez, M. / Garcia, C. / Lillo, M.P. / Mancheno, J.M.

Funding support

Spain, 1items

Citation

Journal: Int.J.Biol.Macromol. / Year: 2023
Title: Atomic crystal structure and sugar specificity of a beta-trefoil lectin domain from the ectomycorrhizal basidiomycete Laccaria bicolor.
Authors: Acebron, I. / Campanero-Rhodes, M.A. / Solis, D. / Menendez, M. / Garcia, C. / Lillo, M.P. / Mancheno, J.M.

History

Deposition	Oct 5, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 22, 2023	Provider: repository / Type: Initial release
Revision 1.1	Feb 7, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	8b97_validation.pdf.gz	1.8 MB	Display	wwPDB validaton report
Full document	8b97_full_validation.pdf.gz	1.8 MB	Display
Data in XML	8b97_validation.xml.gz	11 KB	Display
Data in CIF	8b97_validation.cif.gz	16.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b9/8b97 ftp://data.pdbj.org/pub/pdb/validation_reports/b9/8b97	HTTPS FTP

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Related structure data

Related structure data	8b8fC 2y9fS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#161 - May 2013 Ricin similarity (1) #69 - Sep 2005 Cholera Toxin similarity (1)

Deposited unit

A: Beta-trefoil domain of the LBL lectin

hetero molecules

18.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	52.472, 61.026, 44.549
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2
Space group name Hall	P22ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x+1/2,y+1/2,-z #4: -x,-y,z

Components on special symmetry positions

ID	Model	Components
1	1	A-325- HOH
2	1	A-357- HOH

#1: Protein

Beta-trefoil domain of the LBL lectin

Mass: 16865.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Laccaria bicolor S238N-H53 (fungus) / Strain: S238N-H82 / ATCC MYA-4686 / Gene: LACBIDRAFT_318163 / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B0D650

#2: Polysaccharide

beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

Type: oligosaccharide, Oligosaccharide / Class: Glycan component / Mass: 383.349 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: N-acetyl-alpha-lactosamine

Descriptor	Type	Program
DGalpb1-4DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a4-b1	WURCS	PDB2Glycan 1.1.0
[][a-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}	LINUCS	PDB-CARE

#3: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H₂O

Has ligand of interest

Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.11 Å³/Da / Density % sol: 41.83 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 20% (w/v) PEG 6000, 0.1 M sodium acetate, pH 5.0, and 0.2 M ammonium chloride

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 10, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.939 Å / Relative weight: 1
Reflection	Resolution: 0.97→44.55 Å / Num. obs: 82583 / % possible obs: 97 % / Redundancy: 12.4 % / B_iso Wilson estimate: 4.94 Å² / CC_1/2: 0.998 / CC star: 1 / R_pim(I) all: 0.021 / R_rim(I) all: 0.08 / Net I/σ(I): 31.4
Reflection shell	Resolution: 0.97→1.02 Å / Redundancy: 9.1 % / Mean I/σ(I) obs: 10.9 / Num. unique obs: 9744 / CC_1/2: 0.962 / CC star: 0.99 / R_pim(I) all: 0.071 / % possible all: 80.1

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Processing

Software

Name	Version	Classification
PHENIX	1.19.2_4158	refinement
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2y9f

2y9f

Resolution: 0.97→44.55 Å / SU ML: 0.0558 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 12.0035
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1524	4125	5 %
R_work	0.1405	78404	-
obs	0.1411	82529	96.82 %

Solvent computation

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

Displacement parameters

B_iso mean: 7.95 Å²

Refinement step

Cycle: LAST / Resolution: 0.97→44.55 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1183	0	130	235	1548

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0059	1408
X-RAY DIFFRACTION	f_angle_d	1.145	1938
X-RAY DIFFRACTION	f_chiral_restr	0.0801	228
X-RAY DIFFRACTION	f_plane_restr	0.0143	240
X-RAY DIFFRACTION	f_dihedral_angle_d	7.047	179

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 (%)
0.97-0.98	0.2006	92	0.1729	1833	X-RAY DIFFRACTION	66.79
0.98-0.99	0.1664	120	0.1599	2062	X-RAY DIFFRACTION	74.8
0.99-1.01	0.1681	127	0.1583	2260	X-RAY DIFFRACTION	83.14
1.01-1.02	0.1538	157	0.1448	2455	X-RAY DIFFRACTION	89.39
1.02-1.03	0.151	147	0.1439	2576	X-RAY DIFFRACTION	93.64
1.03-1.05	0.1574	138	0.135	2728	X-RAY DIFFRACTION	99
1.05-1.06	0.1324	164	0.13	2737	X-RAY DIFFRACTION	99.86
1.06-1.08	0.1244	141	0.1299	2762	X-RAY DIFFRACTION	100
1.08-1.1	0.1278	121	0.1248	2778	X-RAY DIFFRACTION	100
1.1-1.12	0.1275	149	0.1281	2779	X-RAY DIFFRACTION	100
1.12-1.14	0.135	136	0.1228	2776	X-RAY DIFFRACTION	100
1.14-1.16	0.1249	140	0.117	2761	X-RAY DIFFRACTION	100
1.16-1.18	0.1489	139	0.1221	2770	X-RAY DIFFRACTION	100
1.18-1.21	0.1115	154	0.1193	2792	X-RAY DIFFRACTION	100
1.21-1.24	0.1187	146	0.1197	2778	X-RAY DIFFRACTION	100
1.24-1.27	0.1187	150	0.1222	2764	X-RAY DIFFRACTION	100
1.27-1.3	0.1364	152	0.1275	2781	X-RAY DIFFRACTION	100
1.3-1.34	0.146	161	0.1256	2765	X-RAY DIFFRACTION	100
1.34-1.38	0.153	128	0.129	2802	X-RAY DIFFRACTION	100
1.38-1.43	0.1523	143	0.1348	2802	X-RAY DIFFRACTION	100
1.43-1.49	0.1167	141	0.127	2805	X-RAY DIFFRACTION	100
1.49-1.56	0.1253	156	0.1298	2792	X-RAY DIFFRACTION	100
1.56-1.64	0.1479	138	0.1305	2818	X-RAY DIFFRACTION	99.97
1.64-1.74	0.1405	126	0.1352	2814	X-RAY DIFFRACTION	100
1.74-1.88	0.1628	153	0.1362	2833	X-RAY DIFFRACTION	100
1.88-2.07	0.1603	147	0.134	2810	X-RAY DIFFRACTION	100
2.07-2.37	0.1765	156	0.1411	2860	X-RAY DIFFRACTION	100
2.37-2.98	0.1826	137	0.1651	2900	X-RAY DIFFRACTION	100
2.98-44.55	0.1796	166	0.1763	3011	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	7.02097423965	-2.78575017639	2.50764836106	6.99583517564	-0.0575601873797	7.33243285119	0.00244280630599	0.35494298759	-0.237354424834	-0.0899597129294	0.00708533569822	-0.357908094862	0.423168425777	0.473844044105	-0.0399622175993	0.0943718088369	-0.0131871350384	0.00949634461925	0.0553063645352	-0.0250421306537	0.089467422491	65.4146553284	-3.18363414677	49.455172229
2	4.26724310678	-3.13424356775	-0.17356737643	4.04068213113	1.68655517326	1.4991670661	0.110371325969	0.13340144211	-0.0930817347953	-0.240875674422	-0.0289317904082	-0.0235438453117	-0.0357133781637	0.045171066951	-0.0832875724487	0.049785826678	-0.00104745178579	0.00710961756466	0.0249785611461	-0.00101561512998	0.0374364074574	54.6019002937	4.23506970079	44.4946113505
3	2.21189546305	-0.493282298852	0.513792527534	1.47524446353	0.357828152455	2.5013624164	0.0215409997246	-0.162450465887	-0.102657391735	0.110555316776	0.0535331437933	0.0934054940977	0.0711543780882	-0.152212403709	-0.0642948949221	0.0249999572909	-0.0047180644411	0.00824728405152	0.0252390681853	0.00495539474426	0.0302358711564	55.1680763333	7.65486562379	59.9645938418
4	1.13618714509	-0.116599840318	-0.130933733406	1.37430178574	-0.475992591303	0.445189706406	9.11696591092E-5	-0.0501841219643	0.0701756499912	0.0647613619763	0.00779995457	0.00906253940255	-0.0624856705571	-0.0125283203262	0.0037301866005	0.021428062019	0.000526940320061	0.000812669527373	0.0165232867942	-0.00794717150262	0.0252115502304	55.1693338254	16.7898292341	56.012035732
5	1.86236788769	-0.671173160097	0.517602885001	2.36895133669	0.421297548552	0.483737672039	0.0039442314746	0.0491182790553	0.335447829764	-0.134964093305	-0.0449625064257	-0.102521601356	-0.146886100159	0.0252276551309	0.0114849790129	0.0540965081353	-0.00592609881032	0.00230797404441	0.0236564260022	-0.00199173143477	0.0665738233348	56.9837925863	24.1965122485	54.6923096042
6	0.809447319954	-0.0674127265108	0.375203850388	0.0767165837831	0.17125740951	1.77063158159	-0.0177958782213	-0.0439752711659	-0.0384342410625	0.0307143099522	-0.00172135330104	0.0526625380027	-0.0282883087307	-0.11936130437	-0.00274090431081	0.0192284529734	0.00266571134442	0.00991997107841	0.022497075214	-0.00624598404166	0.0322134335418	49.1727930035	15.2139396217	56.6094598675
7	0.168755830795	-0.0621771943043	0.13009074667	0.512136396414	-0.157563559414	0.424842588513	0.0231571903854	0.121741658188	-0.0589350119069	-0.103915310059	-0.0486702651446	-0.0434216032127	-0.0195971240789	0.0162027667394	-0.0308266143888	0.0304042632748	-0.0041632919319	0.0122477869152	0.0351105258469	-0.0103581234115	0.0393124334014	61.9984351028	7.70117542653	42.4597108503
8	4.10820165103	-1.86760767268	-1.30435757265	2.4789826063	1.00787992264	1.33319515569	-0.0868708986556	0.0237936998452	-0.0759202907203	-0.0574181194267	0.0706688099373	-0.187007855062	0.0962717703513	0.073930655624	0.0253460395617	0.0401307905318	-0.00362784060847	0.0123886123191	0.0375394052186	-0.00781584002292	0.052612053995	65.5020624392	6.59668822883	43.6824617904
9	2.16564112714	-0.662780998096	0.126665152145	1.23081982328	-0.675218199247	1.73627453522	0.0354000467824	0.131599370136	0.0365309869284	-0.0232783993664	-0.000326239487542	0.0858742740676	-0.040868127653	-0.0500094137924	-0.0236229846029	0.0184171400164	0.000767327661733	0.00275125427448	0.0141548177252	0.00320082612125	0.0327190424897	57.0653796529	17.7610583974	45.2786222622
10	0.0736138729618	-0.277525281365	-0.176284419013	1.29148703098	0.583995534674	1.42796685548	0.0807013854322	-0.0718272554872	0.0757389030753	0.317232985105	-0.128022630378	-0.433631792047	-0.283999161819	0.25958348727	-0.00923220484602	0.0924431309052	-0.0363901862941	-0.0293250566333	0.0522326356905	0.00728255971694	0.0748406800099	71.9551015808	19.0157863757	54.474289015
11	0.930385576217	-0.846699174611	-0.796830713446	2.74356416332	-0.110619899853	1.88534927501	0.114207041206	0.249753229188	0.0965461088141	-0.200020183397	-0.0184634799516	0.0303045584726	-0.14310922987	-0.11656852785	-0.0583473422299	0.0291140122699	-0.00533661257899	-0.000293831502465	0.0618923805001	0.0116021953809	0.0416563380763	64.0288088037	18.7357293099	43.6940720089
12	2.8305968155	1.61034218899	-0.0857602587454	1.99307154455	1.41297446012	2.13463667773	0.0455835590778	0.105486664271	0.049396550783	-0.00653867258436	0.0375883696043	-0.0244326313306	-0.270512073498	-0.00885719047534	-0.000258141890175	0.0208013885817	-0.00155446787292	0.00688907288991	0.0253752778591	0.00715933392507	0.027127345248	71.2831743947	15.4639966372	43.7505078515
13	1.27774096226	1.37167193143	-0.919026434106	4.28527414072	-2.68544520329	1.68531336795	-0.058114246592	0.00781005328944	-0.136891316486	0.0200668376321	-0.0726225987341	-0.202924000554	0.108450195153	0.111392690749	0.105344907511	0.0484856705786	0.00440155734494	0.00459847776692	0.0198285971472	-0.0089829143045	0.0384930584088	67.0778044647	2.50608630093	51.4560195822
14	5.71205037515	0.949805632657	-0.38945814841	5.94574779751	1.74281752115	0.592982340519	-0.0495311433911	-0.6588913558	-0.38977177586	0.396519015873	-0.0513592617692	0.192139294653	0.293719292454	-0.0470032902561	0.0929020082659	0.098387942851	-0.0109906680304	-0.018216421587	0.0367246367155	0.0320522607263	0.155857222622	60.5943711165	-2.94634864509	61.4883895516
15	0.85941542704	0.539886112734	-1.16042294077	0.925416685531	-0.838208393276	2.38866076862	-0.0453420467618	0.0357523934432	-0.0791560207312	-0.0771639921712	0.00892065044248	-0.159406616825	0.121164220123	0.188062118276	0.0313629821337	0.0507203932218	0.00939747053702	-0.00386773383932	0.0246888103369	-0.00984194986673	0.0321747286427	68.316852847	4.82321584317	53.8990164343
16	1.43759540862	0.319498124692	-0.629109395823	0.744858632044	-0.0916383057923	1.9298458865	-0.0591274428008	-0.00486002980427	0.00982889701884	-0.00956326279692	0.0181174704594	-0.0844583084253	0.0666663731133	0.153112229799	0.0223250973412	0.0215486031151	0.00188739235333	-0.00661760618341	0.0254546166321	0.00267467556984	0.0229650540936	69.2052655453	10.7922327909	57.9406220734
17	1.23346795511	-0.801977727226	-0.446971858107	0.547449609804	0.305806139929	2.40081175107	-0.100102518334	-0.241446663022	0.319641088614	0.185625257437	0.0641866737855	-0.160029474534	-0.205158706899	-0.112647101427	0.00890132119299	0.0649119197031	0.00987923507982	-0.0174865251802	0.0604903437165	-0.0308289207159	0.0636856075817	62.6630446353	17.8700039546	65.4886651469
18	1.53135013107	0.484993264742	-1.13813927734	0.968309310038	0.338442540146	2.2917997872	-0.0100178073638	-0.0749862508848	-0.195656676335	0.11793280991	0.00672504433776	-0.183114139238	0.168526770914	0.281873663983	0.00357828848002	0.0424355016646	0.00914618303904	-0.0217408205043	0.0678419527314	-0.00146031018372	0.060682200588	73.9155647664	7.97271651692	61.1698805931
19	2.12370212929	-0.10264853015	0.904035204248	1.34538017938	0.061014575495	2.34823598973	0.0868132899392	-0.0849368581665	-0.136661885206	0.0995433298421	-0.0260176692524	-0.100344974644	0.165644727481	0.0936773265687	-0.00793688853252	0.0449396221086	0.00147986480947	-0.0148096383019	0.0271161872107	0.00190548659895	0.0353450235949	65.3186335579	4.62802839923	62.9187311579
20	3.43324778817	0.361502542513	2.14319763519	1.30617467621	0.500410152565	3.13601573341	0.015066669174	-0.201622444825	0.160509878465	0.0437493483825	0.0359394127216	0.40249978495	0.166545680311	-0.33532786701	-0.0473843903538	0.0381443625981	-0.029847924273	-0.0321724508092	0.0475655730053	0.00691877390249	0.128334306	50.8987780776	3.95163754039	53.0261298927

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

ID	Refine TLS-ID	Selection details	Auth seq-ID	Label seq-ID
1	1	(chain A and resid 2:6)	2 - 6	1 - 5
2	2	(chain A and resid 7:13)	7 - 13	6 - 12
3	3	(chain A and resid 14:21)	14 - 21	13 - 20
4	4	(chain A and resid 22:27)	22 - 27	21 - 26
5	5	(chain A and resid 28:35)	28 - 35	27 - 34
6	6	(chain A and resid 36:46)	36 - 46	35 - 45
7	7	(chain A and resid 47:56)	47 - 56	46 - 55
8	8	(chain A and resid 57:64)	57 - 64	56 - 63
9	9	(chain A and resid 65:72)	65 - 72	64 - 71
10	10	(chain A and resid 73:82)	73 - 82	72 - 81
11	11	(chain A and resid 83:89)	83 - 89	82 - 88
12	12	(chain A and resid 90:94)	90 - 94	89 - 93
13	13	(chain A and resid 95:102)	95 - 102	94 - 101
14	14	(chain A and resid 103:108)	103 - 108	102 - 107
15	15	(chain A and resid 109:114)	109 - 114	108 - 113
16	16	(chain A and resid 115:123)	115 - 123	114 - 122
17	17	(chain A and resid 124:133)	124 - 133	123 - 132
18	18	(chain A and resid 134:140)	134 - 140	133 - 139
19	19	(chain A and resid 141:147)	141 - 147	140 - 146
20	20	(chain A and resid 148:152)	148 - 152	147 - 151

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