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- PDB-6htn: Structure of a fucose lectin from Kordia zhangzhouensis in comple... -

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Basic information

Entry
Database: PDB / ID: 6htn
TitleStructure of a fucose lectin from Kordia zhangzhouensis in complex with methyl-fucoside
ComponentsFucose-binding lectin
KeywordsSUGAR BINDING PROTEIN / lectin / propeller / fucose binding
Function / homology
Function and homology information


carbohydrate binding
Similarity search - Function
Fucose-specific lectin / Fucose-specific lectin / Fungal fucose-specific lectin / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
methyl alpha-L-fucopyranoside / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / Fucose-binding lectin
Similarity search - Component
Biological speciesKordia periserrulae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsVarrot, A.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-15-IDEX-02 France
CitationJournal: Structure / Year: 2019
Title: Architecture and Evolution of Blade Assembly in beta-propeller Lectins.
Authors: Bonnardel, F. / Kumar, A. / Wimmerova, M. / Lahmann, M. / Perez, S. / Varrot, A. / Lisacek, F. / Imberty, A.
History
DepositionOct 4, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 29, 2020Group: 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.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3May 1, 2024Group: 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fucose-binding lectin
B: Fucose-binding lectin
C: Fucose-binding lectin
D: Fucose-binding lectin
E: Fucose-binding lectin
F: Fucose-binding lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,01836
Polymers97,4216
Non-polymers4,59730
Water23,1851287
1
A: Fucose-binding lectin
B: Fucose-binding lectin
C: Fucose-binding lectin
D: Fucose-binding lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,17725
Polymers64,9474
Non-polymers3,23021
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Fucose-binding lectin
F: Fucose-binding lectin
hetero molecules

E: Fucose-binding lectin
F: Fucose-binding lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,68222
Polymers64,9474
Non-polymers2,73518
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575x,-y+2,-z1
Unit cell
Length a, b, c (Å)87.102, 90.522, 143.777
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11E-504-

HOH

21F-524-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 2 - 144 / Label seq-ID: 2 - 144

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14AA
24EE
15AA
25FF
16BB
26CC
17BB
27DD
18BB
28EE
19BB
29FF
110CC
210DD
111CC
211EE
112CC
212FF
113DD
213EE
114DD
214FF
115EE
215FF

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

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Protein / Sugars , 2 types, 24 molecules ABCDEF

#1: Protein
Fucose-binding lectin


Mass: 16236.863 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: N terminal methionine cleaved off / Source: (gene. exp.) Kordia periserrulae (bacteria) / Gene: C8N46_102337 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A2T6C3M6
#2: Sugar
ChemComp-MFU / methyl alpha-L-fucopyranoside / ALPHA-L-METHYL-FUCOSE / methyl 6-deoxy-alpha-L-galactopyranoside / methyl alpha-L-fucoside / methyl L-fucoside / methyl fucoside


Type: L-saccharide / Mass: 178.183 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Formula: C7H14O5
IdentifierTypeProgram
LFucp[1Me]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-a-L-fucopyranoseCOMMON NAMEGMML 1.0
o1-methyl-a-L-fucoseIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 1299 molecules

#3: Chemical
ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL


Mass: 370.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O9
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1287 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.1 % / Description: parallelepipoid
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Morpheus 1 box 1 solution 40 for Mefuc complex or 35% PEG smear medium 10% isopropanol for complex with selenofucoside

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.55→39.25 Å / Num. obs: 165158 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.031 / Rrim(I) all: 0.051 / Χ2: 0.91 / Net I/σ(I): 16.9
Reflection shellResolution: 1.55→1.57 Å / Redundancy: 5 % / Rmerge(I) obs: 0.654 / Num. unique obs: 7950 / CC1/2: 0.773 / Rpim(I) all: 0.496 / Rrim(I) all: 0.824 / Χ2: 0.81 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
PDB_EXTRACT3.22data extraction
XDS20180126data reduction
Aimless0.7.2data scaling
SHELXD2016.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SAD model

Resolution: 1.55→39.25 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.348 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.067 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18002 8260 5 %RANDOM
Rwork0.15536 ---
obs0.15659 156839 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.131 Å2
Baniso -1Baniso -2Baniso -3
1--0.78 Å20 Å2-0 Å2
2---0.5 Å20 Å2
3---1.28 Å2
Refinement stepCycle: 1 / Resolution: 1.55→39.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6824 0 309 1287 8420
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0137550
X-RAY DIFFRACTIONr_bond_other_d0.0010.0186437
X-RAY DIFFRACTIONr_angle_refined_deg1.8021.66610307
X-RAY DIFFRACTIONr_angle_other_deg1.6241.62814967
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5925904
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.36523.545378
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.379151102
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.6671524
X-RAY DIFFRACTIONr_chiral_restr0.0990.2996
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.028494
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021698
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8052.0463556
X-RAY DIFFRACTIONr_mcbond_other1.8032.0463555
X-RAY DIFFRACTIONr_mcangle_it2.483.0714480
X-RAY DIFFRACTIONr_mcangle_other2.4793.0714481
X-RAY DIFFRACTIONr_scbond_it2.6562.213994
X-RAY DIFFRACTIONr_scbond_other2.6562.213995
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7163.2135828
X-RAY DIFFRACTIONr_long_range_B_refined5.12225.1369231
X-RAY DIFFRACTIONr_long_range_B_other5.12125.1389232
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A49520.06
12B49520.06
21A49580.06
22C49580.06
31A49450.06
32D49450.06
41A49380.06
42E49380.06
51A49510.06
52F49510.06
61B49410.07
62C49410.07
71B49580.05
72D49580.05
81B49250.06
82E49250.06
91B49750.05
92F49750.05
101C49240.07
102D49240.07
111C49510.06
112E49510.06
121C49150.06
122F49150.06
131D48600.06
132E48600.06
141D48800.05
142F48800.05
151E49690.07
152F49690.07
LS refinement shellResolution: 1.548→1.588 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 652 -
Rwork0.289 11335 -
obs--98.67 %

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