PDB-8b8f: Atomic structure of the beta-trefoil domain of the Laccaria bicol...

ID or keywords:

Entry

Database: PDB / ID: 8b8f

Title

Atomic structure of the beta-trefoil domain of the Laccaria bicolor lectin LBL in complex with lactose

Components

N-terminal beta-trefoil domain of the lectin LBL from Laccaria bicolor

Keywords

SUGAR BINDING PROTEIN / beta-trefoil / Laccaria bicolor / lectin / polysaccharide / sugar-specificity at atomic resolution

Function / homology

Ricin B-like lectins / beta-lactose / alpha-lactose / Predicted protein

Function and homology information

Biological species

Laccaria bicolor S238N-H53 (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1 Å

Authors

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

Funding support

Spain, 2items

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 4, 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	8b8f_validation.pdf.gz	2.3 MB	Display	wwPDB validaton report
Full document	8b8f_full_validation.pdf.gz	2.3 MB	Display
Data in XML	8b8f_validation.xml.gz	11.3 KB	Display
Data in CIF	8b8f_validation.cif.gz	17 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b8/8b8f ftp://data.pdbj.org/pub/pdb/validation_reports/b8/8b8f	HTTPS FTP

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Related structure data

Related structure data	8b97C 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	#124 - Apr 2010 Concanavalin A and Circular Permutation similarity (2) #69 - Sep 2005 Cholera Toxin similarity (2) #161 - May 2013 Ricin similarity (2)

Deposited unit

A: N-terminal beta-trefoil domain of the lectin LBL from Laccaria bicolor

hetero molecules

18.9 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)	52.530, 61.270, 44.790
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-334- HOH
2	1	A-378- HOH

#1: Protein

N-terminal beta-trefoil domain of the lectin LBL from Laccaria bicolor

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 (E. coli) / References: UniProt: B0D650

#2: Polysaccharide

beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose

Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-lactose

#3: Polysaccharide

beta-D-galactopyranose-(1-4)-beta-D-glucopyranose

Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-lactose

#4: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 258 / 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: 2.14 Å³/Da / Density % sol: 42.44 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting 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: ID23-2 / Wavelength: 0.8726 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 10, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8726 Å / Relative weight: 1
Reflection	Resolution: 1→15.2 Å / Num. obs: 79659 / % possible obs: 100 % / Redundancy: 8 % / B_iso Wilson estimate: 5.67 Å² / CC_1/2: 0.988 / CC star: 0.997 / R_pim(I) all: 0.044 / R_sym value: 0.123 / Net I/σ(I): 10.9
Reflection shell	Resolution: 1→1.05 Å / Num. unique obs: 11493 / CC_1/2: 0.988 / CC star: 0.997 / R_pim(I) all: 0.044 / R_sym value: 0.123

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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: 1→15.2 Å / SU ML: 0.0801 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 12.3186
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1523	3995	5.02 %
R_work	0.1402	75605	-
obs	0.1408	79600	99.98 %

Solvent computation

Shrinkage radii: 0.5 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 9.85 Å²

Refinement step

Cycle: LAST / Resolution: 1→15.2 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1184	0	138	258	1580

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0084	1473
X-RAY DIFFRACTION	f_angle_d	1.2686	2038
X-RAY DIFFRACTION	f_chiral_restr	0.0857	246
X-RAY DIFFRACTION	f_plane_restr	0.0143	250
X-RAY DIFFRACTION	f_dihedral_angle_d	7.1446	193

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 (%)
1-1.01	0.2137	133	0.2126	2538	X-RAY DIFFRACTION	100
1.01-1.02	0.195	125	0.1866	2592	X-RAY DIFFRACTION	100
1.02-1.03	0.1965	150	0.1763	2545	X-RAY DIFFRACTION	100
1.03-1.05	0.1762	147	0.1618	2593	X-RAY DIFFRACTION	100
1.05-1.06	0.1519	126	0.1539	2599	X-RAY DIFFRACTION	99.96
1.06-1.08	0.1732	136	0.1428	2576	X-RAY DIFFRACTION	100
1.08-1.09	0.1451	137	0.1423	2567	X-RAY DIFFRACTION	100
1.09-1.11	0.1533	144	0.1295	2568	X-RAY DIFFRACTION	100
1.11-1.13	0.16	136	0.1397	2594	X-RAY DIFFRACTION	100
1.13-1.15	0.1562	134	0.1302	2574	X-RAY DIFFRACTION	100
1.15-1.17	0.1341	142	0.1358	2616	X-RAY DIFFRACTION	100
1.17-1.19	0.1414	132	0.1348	2581	X-RAY DIFFRACTION	100
1.19-1.21	0.1254	121	0.1282	2585	X-RAY DIFFRACTION	100
1.21-1.24	0.1358	137	0.1276	2579	X-RAY DIFFRACTION	100
1.24-1.27	0.1549	119	0.1324	2613	X-RAY DIFFRACTION	100
1.27-1.3	0.1389	131	0.1335	2592	X-RAY DIFFRACTION	100
1.3-1.34	0.1463	143	0.1323	2616	X-RAY DIFFRACTION	100
1.34-1.38	0.141	144	0.1298	2584	X-RAY DIFFRACTION	100
1.38-1.42	0.1617	146	0.1295	2589	X-RAY DIFFRACTION	99.96
1.42-1.47	0.136	138	0.1318	2600	X-RAY DIFFRACTION	100
1.47-1.53	0.136	122	0.1368	2619	X-RAY DIFFRACTION	100
1.53-1.6	0.1382	178	0.13	2580	X-RAY DIFFRACTION	100
1.6-1.68	0.1708	146	0.1277	2616	X-RAY DIFFRACTION	100
1.68-1.79	0.15	146	0.1343	2614	X-RAY DIFFRACTION	100
1.79-1.93	0.1488	122	0.1309	2659	X-RAY DIFFRACTION	100
1.93-2.12	0.1618	133	0.1311	2647	X-RAY DIFFRACTION	100
2.12-2.43	0.1415	134	0.1409	2667	X-RAY DIFFRACTION	100
2.43-3.05	0.1809	161	0.1529	2675	X-RAY DIFFRACTION	100
3.05-15.2	0.1354	132	0.1482	2827	X-RAY DIFFRACTION	99.56

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	4.28260835712	-5.65539432938	2.25456375739	8.7083386019	-2.27643394386	4.9961412411	0.128309413184	0.26245446899	0.0374778609751	-0.0858940746231	-0.158449551652	-0.198642293436	0.273666468691	0.270195915045	0.00907741048895	0.0722950324655	-0.00976245801669	0.00965584347239	0.05155343431	-0.0143105368567	0.0765538049916	-16.0005055384	-1.68016715564	-18.6576888237
2	1.62272034831	-0.268322954956	0.231373614222	1.54801377295	0.216107837118	0.213540838494	0.0197815591813	-0.00118307230974	-0.0362445920479	-0.0360801914978	-0.00740999064102	0.0182391472709	0.0168094491863	-0.0198475031265	-0.0198413816334	0.0170643614383	-0.00214631868362	0.00552340002282	0.0141258904687	0.00472808331474	0.0274149137365	-24.5023429234	6.95971510335	-13.8261335934
3	0.949779218539	-1.01908451214	0.682105853081	2.46888862962	-0.274374928295	0.913982896732	-0.017946251871	-0.0256405569906	0.0936696780372	0.0158236688722	0.0186869445682	-0.0196100811128	-0.0926566098896	0.0148648149034	0.00453735463986	0.0277575707817	-0.00117890289575	0.00402528435747	0.0232556548651	-0.00442409581045	0.0314309868939	-23.1567544964	20.2981387928	-11.5374678634
4	1.72298159198	-0.378037453905	0.684095385523	2.16527811363	0.480789375935	3.2729210003	-0.0241078083872	-0.0837940271261	-0.136571457185	0.110300689332	-0.00111884359443	0.0195420164726	-0.015015485175	-0.0150072451132	0.0119559127329	0.0273328075381	0.00365800350987	0.00439778940228	0.0167853468551	-0.000566748954195	0.0204833781713	-25.3989299902	15.2461692616	-6.38635680849
5	0.626375362923	0.22750332493	0.407850731716	0.908383012082	-0.140904049188	0.808918969415	0.0249538441997	0.000225950919422	-0.00427888610586	0.0117207927379	-0.0103038219375	0.0713155288756	-0.0605534536975	-0.0913724407361	0.00341595560569	0.018293657716	-0.000583542724628	0.00213174413491	0.0216981582925	-0.000754667076888	0.022535924493	-28.740156458	14.0525183405	-15.2197369882
6	3.07368016731	-0.993495186856	0.755626150412	0.868773770899	-0.499367086679	1.02030186962	0.0133566308905	0.142777571008	0.0464595647179	-0.134776504077	-0.0572473773395	-0.151524919972	-0.0450820655041	0.0248886873219	-0.223008562193	0.0437291863311	-0.00303108642367	0.0219831069594	0.0381843319852	-0.0127934869028	0.0500881935128	-10.8139478819	5.69017474258	-27.1702357679
7	2.3542416208	-2.04039310983	-0.776630355966	2.89465882183	0.569631459591	0.619427310737	-0.00983772457787	0.0641370645932	-0.0382327298625	-0.072414149213	0.0235367234758	-0.0105175601547	0.0274870671398	0.00055942692183	0.00849290668889	0.0276889100263	-0.00445054946296	-0.000122947500999	0.0340855500908	0.00170177137527	0.0272149249582	-18.9291835404	12.7221338099	-22.5499473845
8	3.44739350506	0.0112880282315	2.59034738813	2.60768531617	-0.664819856877	3.1545603414	0.0347792059485	0.00601955126878	0.0070553269711	0.117446305639	-0.0254938181111	-0.0401117848753	-0.117852811603	0.0646671517427	-0.0099030131898	0.0371421526799	-0.00845334318088	0.00729991359716	0.0352844705462	4.28285497093E-5	0.0180036827516	-10.9083476648	16.6593949798	-16.7709502155
9	1.04036906388	-0.105483837173	0.0219392698297	0.0802661072862	0.225639616909	0.746566578954	-0.0195371011836	-0.0271483378774	0.138148059072	0.029827014285	0.100204843262	-0.272721453238	-0.136363030081	0.123016985812	0.350302409475	0.116546387524	-0.0408960257757	-0.0288791877506	0.0644757971331	-0.0124017371981	0.08930253423	-5.56876297892	20.0062718944	-10.6071881223
10	1.92733880899	-0.289934758526	-0.299580921755	4.07355498961	-0.177668686033	3.18598327246	0.0601334080125	0.184606707152	0.0762807482424	-0.0723552025335	0.0352390356681	0.0280923363982	-0.115663371239	-0.0196963418118	-0.0914373429007	0.0204314934828	-0.00605594668277	0.00254819718012	0.0506381987835	0.0119948787613	0.0399412802389	-14.6539150775	19.0708634903	-21.4069630182
11	3.6629896149	0.626120620812	0.791142893129	1.90222000214	1.31461154404	3.11179370119	0.00590539149357	0.132624801231	0.0599930639002	-0.0383850244431	0.0162602228148	-0.0594783111817	-0.129681158092	-0.0333104899371	-0.00460510021561	0.0190183171773	0.00149327417123	0.00764423550666	0.0314964504813	0.00404500773849	0.0195877982618	-8.11191982482	14.2230210897	-23.4578602124
12	0.725677122295	-0.89953213532	1.29055526888	3.48747430433	-3.57716993915	4.19734085143	-0.0169270542143	0.0724306094802	-0.0732693070323	-0.115166203693	-0.0305595012905	-0.151510335643	0.175981691919	0.0906589624949	0.00736808821946	0.0419931062742	0.00362360279213	0.00545279776307	0.0249135933413	-0.00699645709869	0.0384396813492	-11.3972414022	2.99425974448	-15.2760479031
13	4.21067969054	0.224511945017	0.87733832433	2.73603219243	-2.16602454028	2.18268220663	-0.0632528619783	-0.488065325426	-0.327540868318	0.261399222919	0.168238160405	0.179456367	0.394583763809	0.0285188734091	-0.108995535805	0.109230402959	0.0187672407755	0.00198519320406	0.0738832230348	0.0334806245044	0.128572589337	-15.5418952997	-4.20039485692	-5.38002197694
14	0.648638499797	-0.00369091697337	0.253559696093	2.04144793811	-0.107956895075	1.10800394136	0.0711406731793	0.0268166495279	-0.189291363998	-0.0769136853409	-0.0253448488808	0.193805486107	0.154035261281	-0.0101407817052	0.00189215367464	0.0561233284123	0.00168889283977	-0.0147343881097	0.0254860004762	-0.00297802409817	0.0568361251774	-16.432664882	1.3505037004	-10.018047174
15	3.04908363229	-0.432788823483	0.461045487383	6.30147766678	2.81855866043	1.77480915526	-0.0329926748462	-0.22076667962	-0.129378422229	-0.00185060507813	-0.000690761195168	-0.324706619102	0.0222158873757	0.399644342024	0.00388762890825	0.037854991404	0.00611623851699	0.00806559395626	0.0896204059785	0.0121658566555	0.0435966587485	-4.38291561652	7.79164180115	-15.141295979
16	0.700063323601	-0.0709644146662	0.069981352274	1.3443534494	0.986423137005	2.46171328255	-0.0895681833589	-0.169024210253	0.12417613554	0.119164812515	0.045640464189	-0.0254000941263	0.0122532612236	0.0243568356894	0.0163499576306	0.0450462121264	0.00721233167305	-0.01332586075	0.0544933485506	-0.00688467280248	0.0297114835304	-14.1435867505	12.7975104093	-3.40189100243
17	1.33529828403	0.0243431483878	0.774569707487	0.460907604922	-0.914091773403	2.32003703395	-0.140726042371	-0.227802662786	0.394394997778	0.101582165129	-0.0104724138014	-0.156720622839	-0.411909717278	-0.0864717215813	-0.0642018224626	0.0854897852586	-0.00157620090089	-0.0278827401627	0.0540395792069	-0.0216718581836	0.0922115684846	-14.8677622952	18.5489697024	-3.66056017876
18	1.84723119337	0.792816805794	-1.44699604493	3.77511859392	2.26727449081	4.62899395979	-0.0767726780164	-0.181171775276	-0.27317496111	0.302577445761	0.0748830542192	-0.36669166454	0.277017759681	0.43113814219	0.0134110289879	0.0600469099344	0.0114702026045	-0.0201941902831	0.120774820625	0.0064876624636	0.0858710949985	-4.46050684878	8.0069869365	-5.86850013747
19	5.95458393551	-1.08254023127	0.280470482809	1.24482814005	-0.516613379844	2.55258791995	0.0469620886463	-0.233699536461	-0.215120348846	0.145690986574	-0.0384687087461	-0.250173038755	0.219974736313	0.147181430273	0.0441617027375	0.0693897956477	0.0070513944654	-0.0284816365902	0.0578029402869	0.00943109012421	0.0642181822069	-11.1517951808	4.53022950279	-1.35814491208
20	5.47225663893	0.641018362192	2.57333747154	0.900970020939	0.412510254672	2.57958999507	0.0515185077655	-0.0836976772129	-0.0627633502189	-0.00535377144507	0.0185198348647	0.170046022332	0.128407539129	-0.12015524004	-0.0571413833769	0.0427466073387	-0.00897887375736	-0.0159512045067	0.0300249450286	0.00502786343742	0.0586252963626	-22.500244972	4.25943799041	-10.9476578572

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 3:8)	3 - 8	2 - 7
2	2	(chain A and resid 9:20)	9 - 20	8 - 19
3	3	(chain A and resid 21:34)	21 - 34	20 - 33
4	4	(chain A and resid 35:39)	35 - 39	34 - 38
5	5	(chain A and resid 40:50)	40 - 50	39 - 49
6	6	(chain A and resid 51:57)	51 - 57	50 - 56
7	7	(chain A and resid 58:70)	58 - 70	57 - 69
8	8	(chain A and resid 71:75)	71 - 75	70 - 74
9	9	(chain A and resid 76:81)	76 - 81	75 - 80
10	10	(chain A and resid 82:88)	82 - 88	81 - 87
11	11	(chain A and resid 89:95)	89 - 95	88 - 94
12	12	(chain A and resid 96:99)	96 - 99	95 - 98
13	13	(chain A and resid 100:105)	100 - 105	99 - 104
14	14	(chain A and resid 106:111)	106 - 111	105 - 110
15	15	(chain A and resid 112:117)	112 - 117	111 - 116
16	16	(chain A and resid 118:127)	118 - 127	117 - 126
17	17	(chain A and resid 128:133)	128 - 133	127 - 132
18	18	(chain A and resid 134:139)	134 - 139	133 - 138
19	19	(chain A and resid 140:144)	140 - 144	139 - 143
20	20	(chain A and resid 145:152)	145 - 152	144 - 151

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